
Bioinformatics () is an
interdisciplinary
Interdisciplinarity or interdisciplinary studies involves the combination of multiple academic disciplines into one activity (e.g., a research project). It draws knowledge from several other fields like sociology, anthropology, psychology, ec ...
field that develops methods and
software tools for understanding
biological
Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process hereditary ...
data, in particular when the data sets are large and complex. As an interdisciplinary field of
science
Science is a systematic endeavor that Scientific method, builds and organizes knowledge in the form of Testability, testable explanations and predictions about the universe.
Science may be as old as the human species, and some of the earli ...
, bioinformatics combines
biology
Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process hereditar ...
,
chemistry,
physics
Physics is the natural science that studies matter, its fundamental constituents, its motion and behavior through space and time, and the related entities of energy and force. "Physical science is that department of knowledge which rel ...
,
computer science
Computer science is the study of computation, automation, and information. Computer science spans theoretical disciplines (such as algorithms, theory of computation, information theory, and automation) to practical disciplines (includin ...
,
information engineering,
mathematics and
statistics to analyze and interpret the
biological data Biological data refers to a compound or information derived from living organisms and their products. A medicinal compound made from living organisms, such as a serum or a vaccine, could be characterized as biological data. Biological data is highly ...
. Bioinformatics has been used for ''
in silico
In biology and other experimental sciences, an ''in silico'' experiment is one performed on computer or via computer simulation. The phrase is pseudo-Latin for 'in silicon' (correct la, in silicio), referring to silicon in computer chips. It ...
'' analyses of biological queries using computational and statistical techniques.
Bioinformatics includes biological studies that use
computer programming
Computer programming is the process of performing a particular computation (or more generally, accomplishing a specific computing result), usually by designing and building an executable computer program. Programming involves tasks such as anal ...
as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of
genomics
Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dim ...
. Common uses of bioinformatics include the identification of candidates
gene
In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...
s and single
nucleotide
Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecul ...
polymorphisms (
SNPs
In genetics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in a sufficiently larg ...
). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties (esp. in agricultural species), or differences between populations. In a less formal way, bioinformatics also tries to understand the organizational principles within
nucleic acid
Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main ...
and
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...
sequences, called
proteomics
Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In ...
.
Image and
signal processing
Signal processing is an electrical engineering subfield that focuses on analyzing, modifying and synthesizing '' signals'', such as sound, images, and scientific measurements. Signal processing techniques are used to optimize transmissions, ...
allow extraction of useful results from large amounts of raw data. In the field of genetics, it aids in sequencing and annotating genomes and their observed
mutation
In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, m ...
s. It plays a role in the
text mining
Text mining, also referred to as ''text data mining'', similar to text analytics, is the process of deriving high-quality information from text. It involves "the discovery by computer of new, previously unknown information, by automatically extract ...
of biological literature and the development of biological and gene
ontologies to organize and query biological data. It also plays a role in the analysis of gene and protein expression and regulation. Bioinformatics tools aid in comparing, analyzing and interpreting genetic and genomic data and more generally in the understanding of evolutionary aspects of molecular biology. At a more integrative level, it helps analyze and catalogue the biological pathways and networks that are an important part of
systems biology
Systems biology is the computational modeling, computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological syst ...
. In
structural biology
Structural biology is a field that is many centuries old which, and as defined by the Journal of Structural Biology, deals with structural analysis of living material (formed, composed of, and/or maintained and refined by living cells) at every le ...
, it aids in the simulation and modeling of DNA,
RNA,
[ proteins as well as biomolecular interactions.
]
History
Historically, the term ''bioinformatics'' did not mean what it means today. Paulien Hogeweg
Paulien Hogeweg (born 1943) is a Dutch theoretical biologist and complex systems researcher studying biological systems as dynamic information processing systems at many interconnected levels. In 1970, together with Ben Hesper, she defined the te ...
and Ben Hesper
Ben is frequently used as a shortened version of the given names Benjamin, Benedict, Bennett or Benson, and is also a given name in its own right.
Ben (in he, בֶּן, ''son of'') forms part of Hebrew surnames, e.g. Abraham ben Abraham ( h ...
coined it in 1970 to refer to the study of information processes in biotic systems. This definition placed bioinformatics as a field parallel to biochemistry
Biochemistry or biological chemistry is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be divided into three fields: structural biology, enzymology ...
(the study of chemical processes in biological systems).[
]
Sequences
There has been a tremendous advance in speed and cost reduction since the completion of the Human Genome Project, with some labs able to sequence over 100,000 billion bases each year, and a full genome can be sequenced for a thousand dollars or less. Computers became essential in molecular biology when protein sequences became available after Frederick Sanger
Frederick Sanger (; 13 August 1918 – 19 November 2013) was an English biochemist who received the Nobel Prize in Chemistry twice.
He won the 1958 Chemistry Prize for determining the amino acid sequence of insulin and numerous other pr ...
determined the sequence of insulin
Insulin (, from Latin ''insula'', 'island') is a peptide hormone produced by beta cells of the pancreatic islets encoded in humans by the ''INS'' gene. It is considered to be the main anabolic hormone of the body. It regulates the metabol ...
in the early 1950s. Comparing multiple sequences manually turned out to be impractical. A pioneer in the field was Margaret Oakley Dayhoff. She compiled one of the first protein sequence databases, initially published as books and pioneered methods of sequence alignment and molecular evolution
Molecular evolution is the process of change in the sequence composition of cell (biology), cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and popula ...
. Another early contributor to bioinformatics was Elvin A. Kabat, who pioneered biological sequence analysis in 1970 with his comprehensive volumes of antibody sequences released with Tai Te Wu between 1980 and 1991.
In the 1970s, new techniques for sequencing DNA were applied to bacteriophage MS2 and øX174, and the extended nucleotide sequences were then parsed with informational and statistical algorithms. These studies illustrated that well known features, such as the coding segments and the triplet code, are revealed in straightforward statistical analyses and were thus proof of the concept that bioinformatics would be insightful.
Goals
To study how normal cellular activities are altered in different disease states, the biological data must be combined to form a comprehensive picture of these activities. Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data. This also includes nucleotide and amino acid sequences, protein domain
In molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist o ...
s, and protein structure
Protein structure is the molecular geometry, three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single ami ...
s. The actual process of analyzing and interpreting data is referred to as computational biology
Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has fo ...
. Important sub-disciplines within bioinformatics and computational biology include:
* Development and implementation of computer programs that enable efficient access to, management, and use of, various types of information.
* Development of new algorithms (mathematical formulas) and statistical measures that assess relationships among members of large data sets. For example, there are methods to locate a gene
In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...
within a sequence, to predict protein structure and/or function, and to cluster
may refer to:
Science and technology Astronomy
* Cluster (spacecraft), constellation of four European Space Agency spacecraft
* Asteroid cluster, a small asteroid family
* Cluster II (spacecraft), a European Space Agency mission to study th ...
protein sequences into families of related sequences.
The primary goal of bioinformatics is to increase the understanding of biological processes. What sets it apart from other approaches, however, is its focus on developing and applying computationally intensive techniques to achieve this goal. Examples include: pattern recognition
Pattern recognition is the automated recognition of patterns and regularities in data. It has applications in statistical data analysis, signal processing, image analysis, information retrieval, bioinformatics, data compression, computer graphic ...
, data mining, machine learning
Machine learning (ML) is a field of inquiry devoted to understanding and building methods that 'learn', that is, methods that leverage data to improve performance on some set of tasks. It is seen as a part of artificial intelligence.
Machine ...
algorithms, and visualization
Visualization or visualisation may refer to:
* Visualization (graphics), the physical or imagining creation of images, diagrams, or animations to communicate a message
* Data visualization, the graphic representation of data
* Information visualiz ...
. Major research efforts in the field include sequence alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Ali ...
, gene finding
In computational biology, gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other function ...
, genome assembly, drug design
Drug design, often referred to as rational drug design or simply rational design, is the inventive process of finding new medications based on the knowledge of a biological target. The drug is most commonly an organic small molecule that ac ...
, drug discovery
In the fields of medicine, biotechnology and pharmacology, drug discovery is the process by which new candidate medications are discovered.
Historically, drugs were discovered by identifying the active ingredient from traditional remedies or by ...
, protein structure alignment, protein structure prediction
Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its secondary and tertiary structure from primary structure. Structure prediction is differen ...
, prediction of gene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. ...
and protein–protein interaction
Protein–protein interactions (PPIs) are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding and th ...
s, genome-wide association studies
In genomics, a genome-wide association study (GWA study, or GWAS), also known as whole genome association study (WGA study, or WGAS), is an observational study of a genome-wide set of genetic variants in different individuals to see if any varian ...
, the modeling of evolution
Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...
and cell division/mitosis.
Bioinformatics now entails the creation and advancement of databases, algorithms, computational and statistical techniques, and theory to solve formal and practical problems arising from the management and analysis of biological data.
Over the past few decades, rapid developments in genomic and other molecular research technologies and developments in information technologies
Information technology (IT) is the use of computers to create, process, store, retrieve, and exchange all kinds of data . and information. IT forms part of information and communications technology (ICT). An information technology system ( ...
have combined to produce a tremendous amount of information related to molecular biology. Bioinformatics is the name given to these mathematical and computing approaches used to glean understanding of biological processes.
Common activities in bioinformatics include mapping and analyzing DNA and protein sequences, aligning DNA and protein sequences to compare them, and creating and viewing 3-D models of protein structures.
Relation to other fields
Bioinformatics is a science field that is similar to but distinct from biological computation, while it is often considered synonymous to computational biology
Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has fo ...
. Biological computation uses bioengineering
Biological engineering or
bioengineering is the application of principles of biology and the tools of engineering to create usable, tangible, economically-viable products. Biological engineering employs knowledge and expertise from a number o ...
and biology
Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process hereditar ...
to build biological computers, whereas bioinformatics uses computation to better understand biology. Bioinformatics and computational biology involve the analysis of biological data, particularly DNA, RNA, and protein sequences. The field of bioinformatics experienced explosive growth starting in the mid-1990s, driven largely by the Human Genome Project
The Human Genome Project (HGP) was an international scientific research project with the goal of determining the base pairs that make up human DNA, and of identifying, mapping and sequencing all of the genes of the human genome from both a ...
and by rapid advances in DNA sequencing technology.
Analyzing biological data to produce meaningful information involves writing and running software programs that use algorithm
In mathematics and computer science, an algorithm () is a finite sequence of rigorous instructions, typically used to solve a class of specific problems or to perform a computation. Algorithms are used as specifications for performing ...
s from graph theory
In mathematics, graph theory is the study of '' graphs'', which are mathematical structures used to model pairwise relations between objects. A graph in this context is made up of '' vertices'' (also called ''nodes'' or ''points'') which are conn ...
, artificial intelligence
Artificial intelligence (AI) is intelligence—perceiving, synthesizing, and inferring information—demonstrated by machine
A machine is a physical system using Power (physics), power to apply Force, forces and control Motion, moveme ...
, soft computing
Soft computing is a set of algorithms,
including neural networks, fuzzy logic, and evolutionary algorithms.
These algorithms are tolerant of imprecision, uncertainty, partial truth and approximation.
It is contrasted with hard computing: al ...
, data mining, image processing
An image is a visual representation of something. It can be two-dimensional, three-dimensional, or somehow otherwise feed into the visual system to convey information. An image can be an artifact, such as a photograph or other two-dimension ...
, and computer simulation
Computer simulation is the process of mathematical modelling, performed on a computer, which is designed to predict the behaviour of, or the outcome of, a real-world or physical system. The reliability of some mathematical models can be dete ...
. The algorithms in turn depend on theoretical foundations such as discrete mathematics
Discrete mathematics is the study of mathematical structures that can be considered "discrete" (in a way analogous to discrete variables, having a bijection with the set of natural numbers) rather than "continuous" (analogously to continu ...
, control theory
Control theory is a field of mathematics that deals with the control of dynamical systems in engineered processes and machines. The objective is to develop a model or algorithm governing the application of system inputs to drive the system to a ...
, system theory
Systems theory is the interdisciplinary study of systems, i.e. cohesive groups of interrelated, interdependent components that can be natural or human-made. Every system has causal boundaries, is influenced by its context, defined by its structu ...
, information theory
Information theory is the scientific study of the quantification, storage, and communication of information. The field was originally established by the works of Harry Nyquist and Ralph Hartley, in the 1920s, and Claude Shannon in the 1940s. ...
, and statistics.
Sequence analysis
Since the Phage Φ-X174 was sequenced in 1977, the DNA sequence
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. Th ...
s of thousands of organisms have been decoded and stored in databases. This sequence information is analyzed to determine genes that encode protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...
s, RNA genes, regulatory sequences, structural motifs, and repetitive sequences. A comparison of genes within a species
In biology, a species is the basic unit of Taxonomy (biology), classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of ...
or between different species can show similarities between protein functions, or relations between species (the use of molecular systematics
Molecular phylogenetics () is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominantly in DNA sequences, to gain information on an organism's evolutionary relationships. From these analyses, it is possible to ...
to construct phylogenetic trees). With the growing amount of data, it long ago became impractical to analyze DNA sequences manually. Computer program
A computer program is a sequence or set of instructions in a programming language for a computer to execute. Computer programs are one component of software, which also includes documentation and other intangible components.
A computer progra ...
s such as BLAST are used routinely to search sequences—as of 2008, from more than 260,000 organisms, containing over 190 billion nucleotide
Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecul ...
s.
DNA sequencing
Before sequences can be analyzed they have to be obtained from the data storage bank example Genbank. DNA sequencing is still a non-trivial problem as the raw data may be noisy or affected by weak signals. Algorithm
In mathematics and computer science, an algorithm () is a finite sequence of rigorous instructions, typically used to solve a class of specific problems or to perform a computation. Algorithms are used as specifications for performing ...
s have been developed for base calling Base calling is the process of assigning nucleobases to chromatogram peaks, light intensity signals, or electrical current changes resulting from nucleotides passing through a nanopore. One computer program for accomplishing this job is Phred, whic ...
for the various experimental approaches to DNA sequencing.
Sequence assembly
Most DNA sequencing techniques produce short fragments of sequence that need to be assembled to obtain complete gene or genome sequences. The so-called shotgun sequencing technique (which was used, for example, by The Institute for Genomic Research
The J. Craig Venter Institute (JCVI) is a non-profit genomics research institute founded by J. Craig Venter, Ph.D. in October 2006. The institute was the result of consolidating four organizations: the Center for the Advancement of G ...
(TIGR) to sequence the first bacterial genome, ''Haemophilus influenzae
''Haemophilus influenzae'' (formerly called Pfeiffer's bacillus or ''Bacillus influenzae'') is a Gram-negative, non-motile, coccobacillary, facultatively anaerobic, capnophilic pathogenic bacterium of the family Pasteurellaceae. The bacte ...
'') generates the sequences of many thousands of small DNA fragments (ranging from 35 to 900 nucleotides long, depending on the sequencing technology). The ends of these fragments overlap and, when aligned properly by a genome assembly program, can be used to reconstruct the complete genome. Shotgun sequencing yields sequence data quickly, but the task of assembling the fragments can be quite complicated for larger genomes. For a genome as large as the human genome
The human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. These are usually treated separately as the ...
, it may take many days of CPU time on large-memory, multiprocessor computers to assemble the fragments, and the resulting assembly usually contains numerous gaps that must be filled in later. Shotgun sequencing is the method of choice for virtually all genomes sequenced today, and genome assembly algorithms are a critical area of bioinformatics research.
Genome annotation
In the context of genomics
Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dim ...
, annotation
An annotation is extra information associated with a particular point in a document or other piece of information. It can be a note that includes a comment or explanation. Annotations are sometimes presented in the margin of book pages. For anno ...
is the process of marking the genes and other biological features in a DNA sequence. This process needs to be automated because most genomes are too large to annotate by hand, not to mention the desire to annotate as many genomes as possible, as the rate of sequencing
In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succi ...
has ceased to pose a bottleneck. Annotation is made possible by the fact that genes have recognisable start and stop regions, although the exact sequence found in these regions can vary between genes.
Genome annotation can be classified into three levels: the nucleotide, protein, and process levels.
Gene finding is a chief aspect of nucleotide-level annotation. For complex genomes, the most successful methods use a combination of ab initio gene prediction and sequence comparison with expressed sequence databases and other organisms. Nucleotide-level annotation also allows the integration of genome sequence with other genetic and physical maps of the genome.
The principal aim of protein-level annotation is to assign function to the products of the genome. Databases of protein sequences and functional domains and motifs are powerful resources for this type of annotation. Nevertheless, half of the predicted proteins in a new genome sequence tend to have no obvious function.
Understanding the function of genes and their products in the context of cellular and organismal physiology is the goal of process-level annotation. One of the obstacles to this level of annotation has been the inconsistency of terms used by different model systems. The Gene Ontology Consortium is helping to solve this problem.
The first description of a comprehensive genome annotation system was published in 1995[ by the team at ]The Institute for Genomic Research
The J. Craig Venter Institute (JCVI) is a non-profit genomics research institute founded by J. Craig Venter, Ph.D. in October 2006. The institute was the result of consolidating four organizations: the Center for the Advancement of G ...
that performed the first complete sequencing and analysis of the genome of a free-living organism, the bacterium ''Haemophilus influenzae
''Haemophilus influenzae'' (formerly called Pfeiffer's bacillus or ''Bacillus influenzae'') is a Gram-negative, non-motile, coccobacillary, facultatively anaerobic, capnophilic pathogenic bacterium of the family Pasteurellaceae. The bacte ...
''.[ ]Owen White
Owen White is a bioinformatician and director of the Institute For Genome Sciences at the University of Maryland School of Medicine. He is known for his work on the bioinformatics tools GLIMMER and MUMmer.
Education
White studied biotechnology a ...
designed and built a software system to identify the genes encoding all proteins, transfer RNAs, ribosomal RNAs (and other sites) and to make initial functional assignments. Most current genome annotation systems work similarly, but the programs available for analysis of genomic DNA, such as the GeneMark program trained and used to find protein-coding genes in ''Haemophilus influenzae
''Haemophilus influenzae'' (formerly called Pfeiffer's bacillus or ''Bacillus influenzae'') is a Gram-negative, non-motile, coccobacillary, facultatively anaerobic, capnophilic pathogenic bacterium of the family Pasteurellaceae. The bacte ...
'', are constantly changing and improving.
Following the goals that the Human Genome Project left to achieve after its closure in 2003, a new project developed by the National Human Genome Research Institute in the U.S appeared. The so-called ENCODE
The Encyclopedia of DNA Elements (ENCODE) is a public research project which aims to identify functional elements in the human genome.
ENCODE also supports further biomedical research by "generating community resources of genomics data, software ...
project is a collaborative data collection of the functional elements of the human genome that uses next-generation DNA-sequencing technologies and genomic tiling arrays, technologies able to automatically generate large amounts of data at a dramatically reduced per-base cost but with the same accuracy (base call error) and fidelity (assembly error).
Gene function prediction
While genome annotation is primarily based on sequence similarity (and thus homology), other properties of sequences can be used to predict the function of genes. In fact, most ''gene'' function prediction methods focus on ''protein'' sequences as they are more informative and more feature-rich. For instance, the distribution of hydrophobic amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha ...
s predicts transmembrane segments in proteins. However, protein function prediction can also use external information such as gene (or protein) expression data, protein structure
Protein structure is the molecular geometry, three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single ami ...
, or protein-protein interactions.
Computational evolutionary biology
Evolutionary biology
Evolutionary biology is the subfield of biology that studies the evolutionary processes (natural selection, common descent, speciation) that produced the diversity of life on Earth. It is also defined as the study of the history of life fo ...
is the study of the origin and descent of species
In biology, a species is the basic unit of Taxonomy (biology), classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of ...
, as well as their change over time. Informatics has assisted evolutionary biologists by enabling researchers to:
* trace the evolution of a large number of organisms by measuring changes in their DNA, rather than through physical taxonomy or physiological observations alone,
* compare entire genomes
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding gen ...
, which permits the study of more complex evolutionary events, such as gene duplication
Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene ...
, horizontal gene transfer
Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring ( reproduction). ...
, and the prediction of factors important in bacterial speciation
Speciation is the evolutionary process by which populations evolve to become distinct species. The biologist Orator F. Cook coined the term in 1906 for cladogenesis, the splitting of lineages, as opposed to anagenesis, phyletic evolution withi ...
,
* build complex computational population genetics
Population genetics is a subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and pop ...
models to predict the outcome of the system over time
* track and share information on an increasingly large number of species and organisms
Future work endeavours to reconstruct the now more complex tree of life
The tree of life is a fundamental archetype in many of the world's mythological, religious, and philosophical traditions. It is closely related to the concept of the sacred tree.Giovino, Mariana (2007). ''The Assyrian Sacred Tree: A Histo ...
.
The area of research within computer science
Computer science is the study of computation, automation, and information. Computer science spans theoretical disciplines (such as algorithms, theory of computation, information theory, and automation) to practical disciplines (includin ...
that uses genetic algorithm
In computer science and operations research, a genetic algorithm (GA) is a metaheuristic inspired by the process of natural selection that belongs to the larger class of evolutionary algorithms (EA). Genetic algorithms are commonly used to gen ...
s is sometimes confused with computational evolutionary biology, but the two areas are not necessarily related.
Comparative genomics
The core of comparative genome analysis is the establishment of the correspondence between genes
In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...
( orthology analysis) or other genomic features in different organisms. It is these intergenomic maps that make it possible to trace the evolutionary processes responsible for the divergence of two genomes. A multitude of evolutionary events acting at various organizational levels shape genome evolution. At the lowest level, point mutations affect individual nucleotides. At a higher level, large chromosomal segments undergo duplication, lateral transfer, inversion, transposition, deletion and insertion. Ultimately, whole genomes are involved in processes of hybridization, polyploidization and endosymbiosis
An ''endosymbiont'' or ''endobiont'' is any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship.
(The term endosymbiosis is from the Greek: ἔνδον ''endon'' "withi ...
, often leading to rapid speciation. The complexity of genome evolution poses many exciting challenges to developers of mathematical models and algorithms, who have recourse to a spectrum of algorithmic, statistical and mathematical techniques, ranging from exact, heuristics
A heuristic (; ), or heuristic technique, is any approach to problem solving or self-discovery that employs a practical method that is not guaranteed to be optimal, perfect, or rational, but is nevertheless sufficient for reaching an immediate, ...
, fixed parameter and approximation algorithms
In computer science and operations research, approximation algorithms are efficient algorithms that find approximate solutions to optimization problems (in particular NP-hard problems) with provable guarantees on the distance of the returned solut ...
for problems based on parsimony models to Markov chain Monte Carlo
In statistics, Markov chain Monte Carlo (MCMC) methods comprise a class of algorithms for sampling from a probability distribution. By constructing a Markov chain that has the desired distribution as its equilibrium distribution, one can obtain ...
algorithms for Bayesian analysis
Bayesian inference is a method of statistical inference in which Bayes' theorem is used to update the probability for a hypothesis as more evidence or information becomes available. Bayesian inference is an important technique in statistics, and ...
of problems based on probabilistic models.
Many of these studies are based on the detection of sequence homology
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a sp ...
to assign sequences to protein families
A protein family is a group of evolutionarily related proteins. In many cases, a protein family has a corresponding gene family, in which each gene encodes a corresponding protein with a 1:1 relationship. The term "protein family" should not be ...
.
Pan genomics
Pan genomics is a concept introduced in 2005 by Tettelin and Medini which eventually took root in bioinformatics. Pan genome is the complete gene repertoire of a particular taxonomic group: although initially applied to closely related strains of a species, it can be applied to a larger context like genus, phylum, etc. It is divided in two parts- The Core genome: Set of genes common to all the genomes under study (These are often housekeeping genes vital for survival) and The Dispensable/Flexible Genome: Set of genes not present in all but one or some genomes under study. A bioinformatics tool BPGA can be used to characterize the Pan Genome of bacterial species.
Genetics of disease
With the advent of next-generation sequencing we are obtaining enough sequence data to map the genes of complex diseases including infertility
Infertility is the inability of a person, animal or plant to reproduce by natural means. It is usually not the natural state of a healthy adult, except notably among certain eusocial species (mostly haplodiploid insects). It is the normal st ...
, breast cancer
Breast cancer is cancer that develops from breast tissue. Signs of breast cancer may include a lump in the breast, a change in breast shape, dimpling of the skin, milk rejection, fluid coming from the nipple, a newly inverted nipple, or ...
or Alzheimer's disease. Genome-wide association studies are a useful approach to pinpoint the mutations responsible for such complex diseases. Through these studies, thousands of DNA variants have been identified that are associated with similar diseases and traits. Furthermore, the possibility for genes to be used at prognosis, diagnosis or treatment is one of the most essential applications. Many studies are discussing both the promising ways to choose the genes to be used and the problems and pitfalls of using genes to predict disease presence or prognosis.
Genome-wide association studies have successfully identified thousands of common genetic variants for complex diseases and traits; however, these common variants only explain a small fraction of heritability. Rare variants may account for some of the missing heritability The "missing heritability" problem is the fact that single genetic variations cannot account for much of the heritability of diseases, behaviors, and other phenotypes. This is a problem that has significant implications for medicine, since a person ...
. Large-scale whole genome sequencing
Whole genome sequencing (WGS), also known as full genome sequencing, complete genome sequencing, or entire genome sequencing, is the process of determining the entirety, or nearly the entirety, of the DNA sequence of an organism's genome at a ...
studies have rapidly sequenced millions of whole genomes, and such studies have identified hundreds of millions of rare variants. Functional annotations predict the effect or function of a genetic variant and help to prioritize rare functional variants, and incorporating these annotations can effectively boost the power of genetic association of rare variants analysis of whole genome sequencing studies. Some tools have been developed to provide all-in-one rare variant association analysis for whole-genome sequencing data, including integration of genotype data and their functional annotations, association analysis, result summary and visualization.
Analysis of mutations in cancer
In cancer
Cancer is a group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body. These contrast with benign tumors, which do not spread. Possible signs and symptoms include a lump, abnormal bl ...
, the genomes of affected cells are rearranged in complex or even unpredictable ways. Massive sequencing efforts are used to identify previously unknown point mutation
A point mutation is a genetic mutation where a single nucleotide base is changed, inserted or deleted from a DNA or RNA sequence of an organism's genome. Point mutations have a variety of effects on the downstream protein product—consequences ...
s in a variety of gene
In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...
s in cancer. Bioinformaticians continue to produce specialized automated systems to manage the sheer volume of sequence data produced, and they create new algorithms and software to compare the sequencing results to the growing collection of human genome
The human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. These are usually treated separately as the ...
sequences and germline
In biology and genetics, the germline is the population of a multicellular organism's cells that pass on their genetic material to the progeny (offspring). In other words, they are the cells that form the egg, sperm and the fertilised egg. They ...
polymorphisms. New physical detection technologies are employed, such as oligonucleotide
Oligonucleotides are short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics. Commonly made in the laboratory by solid-phase chemical synthesis, these small bits of nucleic acids ...
microarrays to identify chromosomal gains and losses (called comparative genomic hybridization Comparative genomic hybridization (CGH) is a molecular cytogenetic method for analysing copy number variations (CNVs) relative to ploidy level in the DNA of a test sample compared to a reference sample, without the need for culturing cells. The ai ...
), and single-nucleotide polymorphism
In genetics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in a sufficiently lar ...
arrays to detect known ''point mutations''. These detection methods simultaneously measure several hundred thousand sites throughout the genome, and when used in high-throughput to measure thousands of samples, generate terabyte
The byte is a unit of digital information that most commonly consists of eight bits. Historically, the byte was the number of bits used to encode a single character of text in a computer and for this reason it is the smallest addressable unit ...
s of data per experiment. Again the massive amounts and new types of data generate new opportunities for bioinformaticians. The data is often found to contain considerable variability, or noise
Noise is unwanted sound considered unpleasant, loud or disruptive to hearing. From a physics standpoint, there is no distinction between noise and desired sound, as both are vibrations through a medium, such as air or water. The difference aris ...
, and thus Hidden Markov model
A hidden Markov model (HMM) is a statistical Markov model in which the system being modeled is assumed to be a Markov process — call it X — with unobservable ("''hidden''") states. As part of the definition, HMM requires that there be an ob ...
and change-point analysis methods are being developed to infer real copy number changes.
Two important principles can be used in the analysis of cancer genomes bioinformatically pertaining to the identification of mutations in the exome
The exome is composed of all of the exons within the genome, the sequences which, when transcribed, remain within the mature RNA after introns are removed by RNA splicing. This includes untranslated regions of messenger RNA (mRNA), and coding re ...
. First, cancer is a disease of accumulated somatic mutations in genes. Second cancer contains driver mutations which need to be distinguished from passengers.
With the breakthroughs that this next-generation sequencing technology is providing to the field of Bioinformatics, cancer genomics could drastically change. These new methods and software allow bioinformaticians to sequence many cancer genomes quickly and affordably. This could create a more flexible process for classifying types of cancer by analysis of cancer driven mutations in the genome. Furthermore, tracking of patients while the disease progresses may be possible in the future with the sequence of cancer samples.
Another type of data that requires novel informatics development is the analysis of lesion
A lesion is any damage or abnormal change in the tissue of an organism, usually caused by disease or trauma. ''Lesion'' is derived from the Latin "injury". Lesions may occur in plants as well as animals.
Types
There is no designated classif ...
s found to be recurrent among many tumors.
Gene and protein expression
Analysis of gene expression
The expression of many genes can be determined by measuring mRNA
In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein.
mRNA is created during the ...
levels with multiple techniques including microarrays, expressed cDNA sequence tag (EST) sequencing, serial analysis of gene expression
Serial Analysis of Gene Expression (SAGE) is a transcriptomic technique used by molecular biologists to produce a snapshot of the messenger RNA population in a sample of interest in the form of small tags that correspond to fragments of those tr ...
(SAGE) tag sequencing, massively parallel signature sequencing (MPSS), RNA-Seq
RNA-Seq (named as an abbreviation of RNA sequencing) is a sequencing technique which uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment, analyzing the continuously changing ...
, also known as "Whole Transcriptome Shotgun Sequencing" (WTSS), or various applications of multiplexed in-situ hybridization. All of these techniques are extremely noise-prone and/or subject to bias in the biological measurement, and a major research area in computational biology involves developing statistical tools to separate signal
In signal processing, a signal is a function that conveys information about a phenomenon. Any quantity that can vary over space or time can be used as a signal to share messages between observers. The '' IEEE Transactions on Signal Processing' ...
from noise
Noise is unwanted sound considered unpleasant, loud or disruptive to hearing. From a physics standpoint, there is no distinction between noise and desired sound, as both are vibrations through a medium, such as air or water. The difference aris ...
in high-throughput gene expression studies. Such studies are often used to determine the genes implicated in a disorder: one might compare microarray data from cancerous epithelial
Epithelium or epithelial tissue is one of the four basic types of animal tissue, along with connective tissue, muscle tissue and nervous tissue. It is a thin, continuous, protective layer of compactly packed cells with a little intercellu ...
cells to data from non-cancerous cells to determine the transcripts that are up-regulated and down-regulated in a particular population of cancer cells.
Analysis of protein expression
Protein microarrays and high throughput (HT) mass spectrometry
Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a '' mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is u ...
(MS) can provide a snapshot of the proteins present in a biological sample. Bioinformatics is very much involved in making sense of protein microarray and HT MS data; the former approach faces similar problems as with microarrays targeted at mRNA, the latter involves the problem of matching large amounts of mass data against predicted masses from protein sequence databases, and the complicated statistical analysis of samples where multiple, but incomplete peptides from each protein are detected. Cellular protein localization in a tissue context can be achieved through affinity proteomics
Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In ...
displayed as spatial data based on immunohistochemistry
Immunohistochemistry (IHC) is the most common application of immunostaining. It involves the process of selectively identifying antigens (proteins) in cells of a tissue section by exploiting the principle of antibodies binding specifically to a ...
and tissue microarray
Tissue microarrays (also TMAs) consist of paraffin blocks in which up to 1000 separate tissue cores are assembled in array fashion to allow multiplex histological analysis.
History
The major limitations in molecular clinical analysis of tis ...
s.
Analysis of regulation
Gene regulation
Regulation of gene expression, or gene regulation, includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA). Sophisticated programs of gene expression are wide ...
is the complex orchestration of events by which a signal, potentially an extracellular signal such as a hormone
A hormone (from the Greek participle , "setting in motion") is a class of signaling molecules in multicellular organisms that are sent to distant organs by complex biological processes to regulate physiology and behavior. Hormones are required ...
, eventually leads to an increase or decrease in the activity of one or more protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...
s. Bioinformatics techniques have been applied to explore various steps in this process.
For example, gene expression can be regulated by nearby elements in the genome. Promoter analysis involves the identification and study of sequence motif
In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. For example, an ''N''-glycosylation site motif can be defined as '' ...
s in the DNA surrounding the coding region of a gene. These motifs influence the extent to which that region is transcribed into mRNA. Enhancer elements far away from the promoter can also regulate gene expression, through three-dimensional looping interactions. These interactions can be determined by bioinformatic analysis of chromosome conformation capture
Chromosome conformation capture techniques (often abbreviated to 3C technologies or 3C-based methods) are a set of molecular biology methods used to analyze the spatial organization of chromatin in a cell. These methods quantify the number of int ...
experiments.
Expression data can be used to infer gene regulation: one might compare microarray
A microarray is a multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of genes from a sample (e.g. from a tissue). It is a two-dimensional array on a solid substrate—usually a glass slide or silic ...
data from a wide variety of states of an organism to form hypotheses about the genes involved in each state. In a single-cell organism, one might compare stages of the cell cycle
The cell cycle, or cell-division cycle, is the series of events that take place in a cell that cause it to divide into two daughter cells. These events include the duplication of its DNA ( DNA replication) and some of its organelles, and sub ...
, along with various stress conditions (heat shock, starvation, etc.). One can then apply clustering algorithms to that expression data to determine which genes are co-expressed. For example, the upstream regions (promoters) of co-expressed genes can be searched for over-represented regulatory elements. Examples of clustering algorithms applied in gene clustering are k-means clustering
''k''-means clustering is a method of vector quantization, originally from signal processing, that aims to partition ''n'' observations into ''k'' clusters in which each observation belongs to the cluster with the nearest mean (cluster centers o ...
, self-organizing map
A self-organizing map (SOM) or self-organizing feature map (SOFM) is an unsupervised machine learning technique used to produce a low-dimensional (typically two-dimensional) representation of a higher dimensional data set while preserving the ...
s (SOMs), hierarchical clustering
In data mining and statistics, hierarchical clustering (also called hierarchical cluster analysis or HCA) is a method of cluster analysis that seeks to build a hierarchy of clusters. Strategies for hierarchical clustering generally fall into tw ...
, and consensus clustering methods.
Analysis of cellular organization
Several approaches have been developed to analyze the location of organelles, genes, proteins, and other components within cells. This is relevant as the location of these components affects the events within a cell and thus helps us to predict the behavior of biological systems. A gene ontology
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and g ...
category, ''cellular component'', has been devised to capture subcellular localization in many biological database
Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genom ...
s.
Microscopy and image analysis
Microscopic pictures allow us to locate both organelle
In cell biology, an organelle is a specialized subunit, usually within a cell, that has a specific function. The name ''organelle'' comes from the idea that these structures are parts of cells, as organs are to the body, hence ''organelle,'' t ...
s as well as molecules. It may also help us to distinguish between normal and abnormal cells, e.g. in cancer
Cancer is a group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body. These contrast with benign tumors, which do not spread. Possible signs and symptoms include a lump, abnormal bl ...
.
Protein localization
The localization of proteins helps us to evaluate the role of a protein. For instance, if a protein is found in the nucleus
Nucleus ( : nuclei) is a Latin word for the seed inside a fruit. It most often refers to:
*Atomic nucleus, the very dense central region of an atom
* Cell nucleus, a central organelle of a eukaryotic cell, containing most of the cell's DNA
Nucl ...
it may be involved in gene regulation
Regulation of gene expression, or gene regulation, includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA). Sophisticated programs of gene expression are wide ...
or splicing. By contrast, if a protein is found in mitochondria, it may be involved in respiration or other metabolic processes. Protein localization is thus an important component of protein function prediction
Protein function prediction methods are techniques that bioinformatics researchers use to assign biological or biochemical roles to proteins. These proteins are usually ones that are poorly studied or predicted based on genomic sequence data. Thes ...
. There are well developed protein subcellular localization prediction
Protein subcellular localization prediction (or just protein localization prediction) involves the prediction of where a protein resides in a cell, its subcellular localization.
In general, prediction tools take as input information about a prote ...
resources available, including protein subcellular location databases, and prediction tools.
Nuclear organization of chromatin
Data from high-throughput chromosome conformation capture
Chromosome conformation capture techniques (often abbreviated to 3C technologies or 3C-based methods) are a set of molecular biology methods used to analyze the spatial organization of chromatin in a cell. These methods quantify the number of int ...
experiments, such as Hi-C (experiment)
]
Hi-C (or standard Hi-C) is a high-throughput Genomics, genomic and epigenomic technique first described in 2009 by Lieberman-Aiden et al. to capture chromatin conformation. In general, Hi-C is considered as a derivative of a series of chromoso ...
and ChIA-PET
Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET or ChIA-PETS) is a technique that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and High-throughput sequen ...
, can provide information on the spatial proximity of DNA loci. Analysis of these experiments can determine the three-dimensional structure and nuclear organization
Nuclear organization refers to the spatial distribution of chromatin within a cell nucleus. There are many different levels and scales of nuclear organisation. Chromatin is a higher order structure of DNA.
At the smallest scale, DNA is pa ...
of chromatin. Bioinformatic challenges in this field include partitioning the genome into domains, such as Topologically Associating Domain
A topologically associating domain (TAD) is a self-interacting genomic region, meaning that DNA sequences within a TAD physically interact with each other more frequently than with sequences outside the TAD. The median size of a TAD in mouse cells ...
s (TADs), that are organised together in three-dimensional space.
Structural bioinformatics
Protein structure prediction is another important application of bioinformatics. The amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha ...
sequence of a protein, the so-called primary structure
Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthes ...
, can be easily determined from the sequence on the gene that codes for it. In the vast majority of cases, this primary structure uniquely determines a structure in its native environment. (Of course, there are exceptions, such as the bovine spongiform encephalopathy
Bovine spongiform encephalopathy (BSE), commonly known as mad cow disease, is an incurable and invariably fatal neurodegenerative disease of cattle. Symptoms include abnormal behavior, trouble walking, and weight loss. Later in the course of ...
(mad cow disease) prion
Prions are misfolded proteins that have the ability to transmit their misfolded shape onto normal variants of the same protein. They characterize several fatal and transmissible neurodegenerative diseases in humans and many other animals. It ...
.) Knowledge of this structure is vital in understanding the function of the protein. Structural information is usually classified as one of ''secondary
Secondary may refer to: Science and nature
* Secondary emission, of particles
** Secondary electrons, electrons generated as ionization products
* The secondary winding, or the electrical or electronic circuit connected to the secondary winding i ...
'', ''tertiary
Tertiary ( ) is a widely used but obsolete term for the geologic period from 66 million to 2.6 million years ago.
The period began with the demise of the non- avian dinosaurs in the Cretaceous–Paleogene extinction event, at the start ...
'' and '' quaternary'' structure. A viable general solution to such predictions remains an open problem. Most efforts have so far been directed towards heuristics that work most of the time.
One of the key ideas in bioinformatics is the notion of homology. In the genomic branch of bioinformatics, homology is used to predict the function of a gene: if the sequence of gene ''A'', whose function is known, is homologous to the sequence of gene ''B,'' whose function is unknown, one could infer that B may share A's function. In the structural branch of bioinformatics, homology is used to determine which parts of a protein are important in structure formation and interaction with other proteins. In a technique called homology modeling
Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "''target''" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous p ...
, this information is used to predict the structure of a protein once the structure of a homologous protein is known. Until recently, this remained the only way to predict protein structures reliably. However, a game-changing breakthrough occurred with the release of new deep-learning algorithms-based software called AlphaFold, developed by a bioinformatics team within Google's A.I. research department DeepMind. AlphaFold, during the 14th Critical Assessment of protein Structure Prediction (CASP14) computational protein structure prediction software competition, became the first contender ever to deliver prediction submissions with accuracy competitive with experimental structures in a majority of cases and greatly outperforming all other prediction software methods up to that point. AlphaFold has since released the predicted structures for hundreds of millions of proteins.
One example of this is hemoglobin in humans and the hemoglobin in legumes (leghemoglobin
3rd Leghemoglobin (also leghaemoglobin or legoglobin) is an oxygen-carrying phytoglobin found in the nitrogen-fixing root nodules of leguminous plants. It is produced by these plants in response to the roots being colonized by nitrogen-fixing ...
), which are distant relatives from the same protein superfamily
A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred (see homology). Usually this common ancestry is inferred from structural alignment and mechanistic similarity, even if no sequence similarit ...
. Both serve the same purpose of transporting oxygen in the organism. Although both of these proteins have completely different amino acid sequences, their protein structures are virtually identical, which reflects their near identical purposes and shared ancestor.
Other techniques for predicting protein structure include protein threading and ''de novo'' (from scratch) physics-based modeling.
Another aspect of structural bioinformatics include the use of protein structures for Virtual Screening
Virtual screening (VS) is a computational technique used in drug discovery to search libraries of small molecules in order to identify those structures which are most likely to bind to a drug target, typically a protein receptor or enzyme.
Virt ...
models such as Quantitative Structure-Activity Relationship models and proteochemometric models (PCM). Furthermore, a protein's crystal structure can be used in simulation of for example ligand-binding studies and ''in silico'' mutagenesis studies.
Network and systems biology
''Network analysis'' seeks to understand the relationships within biological network
A biological network is a method of representing systems as complex sets of binary interactions or relations between various biological entities. In general, networks or graphs are used to capture relationships between entities or objects. A typi ...
s such as metabolic
Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cel ...
or protein–protein interaction networks. Although biological networks can be constructed from a single type of molecule or entity (such as genes), network biology often attempts to integrate many different data types, such as proteins, small molecules, gene expression data, and others, which are all connected physically, functionally, or both.
''Systems biology'' involves the use of computer simulation
Computer simulation is the process of mathematical modelling, performed on a computer, which is designed to predict the behaviour of, or the outcome of, a real-world or physical system. The reliability of some mathematical models can be dete ...
s of cellular subsystems (such as the networks of metabolites and enzyme
Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different molecule ...
s that comprise metabolism
Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run c ...
, signal transduction
Signal transduction is the process by which a chemical or physical signal is transmitted through a cell as a series of molecular events, most commonly protein phosphorylation catalyzed by protein kinases, which ultimately results in a cellular ...
pathways and gene regulatory network
A gene (or genetic) regulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins which, in turn, determine the fun ...
s) to both analyze and visualize the complex connections of these cellular processes. Artificial life
Artificial life (often abbreviated ALife or A-Life) is a field of study wherein researchers examine systems related to natural life, its processes, and its evolution, through the use of simulations with computer models, robotics, and biochemist ...
or virtual evolution attempts to understand evolutionary processes via the computer simulation of simple (artificial) life forms.
Molecular interaction networks
Tens of thousands of three-dimensional protein structures have been determined by X-ray crystallography
X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angle ...
and protein nuclear magnetic resonance spectroscopy (protein NMR) and a central question in structural bioinformatics is whether it is practical to predict possible protein–protein interactions only based on these 3D shapes, without performing protein–protein interaction
Protein–protein interactions (PPIs) are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding and th ...
experiments. A variety of methods have been developed to tackle the protein–protein docking
Macromolecular docking is the computational modelling of the quaternary structure of complexes formed by two or more interacting biological macromolecules. Protein–protein complexes are the most commonly attempted targets of such modelling, fol ...
problem, though it seems that there is still much work to be done in this field.
Other interactions encountered in the field include Protein–ligand (including drug) and protein–peptide. Molecular dynamic simulation of movement of atoms about rotatable bonds is the fundamental principle behind computational algorithm
In mathematics and computer science, an algorithm () is a finite sequence of rigorous instructions, typically used to solve a class of specific problems or to perform a computation. Algorithms are used as specifications for performing ...
s, termed docking algorithms, for studying molecular interactions.
Others
Literature analysis
The growth in the number of published literature makes it virtually impossible to read every paper, resulting in disjointed sub-fields of research. Literature analysis aims to employ computational and statistical linguistics to mine this growing library of text resources. For example:
* Abbreviation recognition – identify the long-form and abbreviation of biological terms
* Named-entity recognition
Named-entity recognition (NER) (also known as (named) entity identification, entity chunking, and entity extraction) is a subtask of information extraction that seeks to locate and classify named entities mentioned in unstructured text into pre- ...
– recognizing biological terms such as gene names
* Protein–protein interaction – identify which protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...
s interact with which proteins from text
The area of research draws from statistics and computational linguistics
Computational linguistics is an Interdisciplinarity, interdisciplinary field concerned with the computational modelling of natural language, as well as the study of appropriate computational approaches to linguistic questions. In general, comput ...
.
High-throughput image analysis
Computational technologies are used to accelerate or fully automate the processing, quantification and analysis of large amounts of high-information-content biomedical imagery. Modern image analysis
Image analysis or imagery analysis is the extraction of meaningful information from images; mainly from digital images by means of digital image processing techniques. Image analysis tasks can be as simple as reading bar coded tags or as sophi ...
systems augment an observer's ability to make measurements from a large or complex set of images, by improving accuracy
Accuracy and precision are two measures of '' observational error''.
''Accuracy'' is how close a given set of measurements (observations or readings) are to their '' true value'', while ''precision'' is how close the measurements are to each ot ...
, objectivity
Objectivity can refer to:
* Objectivity (philosophy), the property of being independent from perception
** Objectivity (science), the goal of eliminating personal biases in the practice of science
** Journalistic objectivity, encompassing fairne ...
, or speed. A fully developed analysis system may completely replace the observer. Although these systems are not unique to biomedical imagery, biomedical imaging is becoming more important for both diagnostics and research. Some examples are:
* high-throughput and high-fidelity quantification and sub-cellular localization ( high-content screening, cytohistopathology, Bioimage informatics)
* morphometrics
Morphometrics (from Greek μορϕή ''morphe'', "shape, form", and -μετρία ''metria'', "measurement") or morphometry refers to the quantitative analysis of ''form'', a concept that encompasses size and shape. Morphometric analyses are co ...
* clinical image analysis and visualization
* determining the real-time air-flow patterns in breathing lungs of living animals
* quantifying occlusion size in real-time imagery from the development of and recovery during arterial injury
* making behavioral observations from extended video recordings of laboratory animals
* infrared measurements for metabolic activity determination
* inferring clone overlaps in DNA mapping, e.g. the Sulston score The Sulston score is an equation used in DNA mapping to numerically assess the likelihood that a given "fingerprint" similarity between two DNA clones is merely a result of chance. Used as such, it is a test of statistical significance. That is, l ...
High-throughput single cell data analysis
Computational techniques are used to analyse high-throughput, low-measurement single cell data, such as that obtained from flow cytometry
Flow cytometry (FC) is a technique used to detect and measure physical and chemical characteristics of a population of cells or particles.
In this process, a sample containing cells or particles is suspended in a fluid and injected into the fl ...
. These methods typically involve finding populations of cells that are relevant to a particular disease state or experimental condition.
Biodiversity informatics
Biodiversity informatics deals with the collection and analysis of biodiversity
Biodiversity or biological diversity is the variety and variability of life on Earth. Biodiversity is a measure of variation at the genetic ('' genetic variability''), species ('' species diversity''), and ecosystem ('' ecosystem diversity' ...
data, such as taxonomic databases, or microbiome
A microbiome () is the community of microorganisms that can usually be found living together in any given habitat. It was defined more precisely in 1988 by Whipps ''et al.'' as "a characteristic microbial community occupying a reasonably we ...
data. Examples of such analyses include phylogenetics
In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups ...
, niche modelling
Species distribution modelling (SDM), also known as environmental (or ecological) niche modelling (ENM), habitat modelling, predictive habitat distribution modelling, and range mapping uses computer algorithms to predict the distribution of a spec ...
, species richness
Species richness is the number of different species represented in an ecological community, landscape or region. Species richness is simply a count of species, and it does not take into account the abundances of the species or their relative ab ...
mapping, DNA barcoding
DNA barcoding is a method of species identification using a short section of DNA from a specific gene or genes. The premise of DNA barcoding is that by comparison with a reference library of such DNA sections (also called " sequences"), an indi ...
, or species
In biology, a species is the basic unit of Taxonomy (biology), classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of ...
identification tools.
Ontologies and data integration
Biological ontologies are directed acyclic graph
In mathematics, particularly graph theory, and computer science, a directed acyclic graph (DAG) is a directed graph with no directed cycles. That is, it consists of vertices and edges (also called ''arcs''), with each edge directed from one v ...
s of controlled vocabularies
Control may refer to:
Basic meanings Economics and business
* Control (management), an element of management
* Control, an element of management accounting
* Comptroller (or controller), a senior financial officer in an organization
* Controlling ...
. They are designed to capture biological concepts and descriptions in a way that can be easily categorised and analysed with computers. When categorised in this way, it is possible to gain added value from holistic and integrated analysis.
The OBO Foundry was an effort to standardise certain ontologies. One of the most widespread is the Gene ontology
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and g ...
which describes gene function. There are also ontologies which describe phenotypes.
Databases
Databases are essential for bioinformatics research and applications. Many databases exist, covering various information types: for example, DNA and protein sequences, molecular structures, phenotypes and biodiversity. Databases may contain empirical data (obtained directly from experiments), predicted data (obtained from analysis), or, most commonly, both. They may be specific to a particular organism, pathway or molecule of interest. Alternatively, they can incorporate data compiled from multiple other databases. These databases vary in their format, access mechanism, and whether they are public or not.
Some of the most commonly used databases are listed below. For a more comprehensive list, please check the link at the beginning of the subsection.
* Used in biological sequence analysis: Genbank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a part ...
, UniProt
UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived fro ...
* Used in structure analysis: Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, c ...
(PDB)
* Used in finding Protein Families and Motif
Motif may refer to:
General concepts
* Motif (chess composition), an element of a move in the consideration of its purpose
* Motif (folkloristics), a recurring element that creates recognizable patterns in folklore and folk-art traditions
* Moti ...
Finding: InterPro
InterPro is a database of protein families, protein domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them.
The contents of InterPro c ...
, Pfam
Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The most recent version, Pfam 35.0, was released in November 2021 and contains 19,632 families.
Use ...
* Used for Next Generation Sequencing: Sequence Read Archive
* Used in Network Analysis: Metabolic Pathway Databases (KEGG
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis ...
, BioCyc), Interaction Analysis Databases, Functional Networks
* Used in design of synthetic genetic circuits: GenoCAD
GenoCAD is one of the earliest computer assisted design tools for synthetic biology. The software is a bioinformatics tool developed and maintained by GenoFAB, Inc.. GenoCAD facilitates the design of protein expression vectors, artificial gene net ...
Software and tools
Software tools for bioinformatics range from simple command-line tools, to more complex graphical programs and standalone web-services available from various bioinformatics companies or public institutions.
Open-source bioinformatics software
Many free and open-source software
Free and open-source software (FOSS) is a term used to refer to groups of software consisting of both free software and open-source software where anyone is freely licensed to use, copy, study, and change the software in any way, and the source ...
tools have existed and continued to grow since the 1980s. The combination of a continued need for new algorithm
In mathematics and computer science, an algorithm () is a finite sequence of rigorous instructions, typically used to solve a class of specific problems or to perform a computation. Algorithms are used as specifications for performing ...
s for the analysis of emerging types of biological readouts, the potential for innovative ''in silico
In biology and other experimental sciences, an ''in silico'' experiment is one performed on computer or via computer simulation. The phrase is pseudo-Latin for 'in silicon' (correct la, in silicio), referring to silicon in computer chips. It ...
'' experiments, and freely available open code
Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Open ...
bases have helped to create opportunities for all research groups to contribute to both bioinformatics and the range of open-source software available, regardless of their funding arrangements. The open source tools often act as incubators of ideas, or community-supported plug-ins in commercial applications. They may also provide ''de facto
''De facto'' ( ; , "in fact") describes practices that exist in reality, whether or not they are officially recognized by laws or other formal norms. It is commonly used to refer to what happens in practice, in contrast with '' de jure'' ("by l ...
'' standards and shared object models for assisting with the challenge of bioinformation integration.
The range of open-source software packages includes titles such as Bioconductor
Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology.
Bioconductor is based primarily on the statistical R programming ...
, BioPerl
BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It has played an integral role in the Human Genome Project.
Background
BioPerl is an active open source software project sup ...
, Biopython, BioJava, BioJS, BioRuby
BioRuby is a collection of open-source Ruby code, comprising classes for computational molecular biology and bioinformatics. It contains classes for DNA and protein sequence analysis, sequence alignment, biological database parsing, structural biol ...
, Bioclipse
The Bioclipse project is a Java-based, open-source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). It gained scripting functionality in 2009, and a command line version in 2021.
Like any RCP applic ...
, EMBOSS
EMBOSS is a free open source software analysis package developed for the needs of the molecular biology and bioinformatics user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of ...
, .NET Bio
.NET Bio is an open source bioinformatics and genomics library created to enable simple loading, saving and analysis of biological data. It was designed for .NET Standard 2.0 and was part of the Microsoft Biology Initiative in the eScience divisio ...
, Orange
Orange most often refers to:
*Orange (fruit), the fruit of the tree species '' Citrus'' × ''sinensis''
** Orange blossom, its fragrant flower
* Orange (colour), from the color of an orange, occurs between red and yellow in the visible spectrum ...
with its bioinformatics add-on, Apache Taverna, UGENE and GenoCAD
GenoCAD is one of the earliest computer assisted design tools for synthetic biology. The software is a bioinformatics tool developed and maintained by GenoFAB, Inc.. GenoCAD facilitates the design of protein expression vectors, artificial gene net ...
. To maintain this tradition and create further opportunities, the non-profit Open Bioinformatics Foundation
The Open Bioinformatics Foundation is a non-profit, volunteer-run organization focused on supporting open source programming in bioinformatics. The mission of the foundation is to support the development of open source toolkits for bioinformatics, ...
[ have supported the annual Bioinformatics Open Source Conference (BOSC) since 2000.]
Web services in bioinformatics
SOAP
Soap is a salt of a fatty acid used in a variety of cleansing and lubricating products. In a domestic setting, soaps are surfactants usually used for washing, bathing, and other types of housekeeping. In industrial settings, soaps are used ...
- and REST
Rest or REST may refer to:
Relief from activity
* Sleep
** Bed rest
* Kneeling
* Lying (position)
* Sitting
* Squatting position
Structural support
* Structural support
** Rest (cue sports)
** Armrest
** Headrest
** Footrest
Arts and ente ...
-based interfaces have been developed for a wide variety of bioinformatics applications allowing an application running on one computer in one part of the world to use algorithms, data and computing resources on servers in other parts of the world. The main advantages derive from the fact that end users do not have to deal with software and database maintenance overheads.
Basic bioinformatics services are classified by the EBI into three categories: SSS
SSS or Sss may refer to:
Places
* SSS islands, part of the Netherlands Antilles
* Sheerness-on-Sea railway station, Kent, England, National Rail station code
* Siassi's airport IATA code
* Southern Cross railway station (formerly Spencer Street) ...
(Sequence Search Services), MSA (Multiple Sequence Alignment), and BSA (Biological Sequence Analysis). The availability of these service-oriented bioinformatics resources demonstrate the applicability of web-based bioinformatics solutions, and range from a collection of standalone tools with a common data format under a single, standalone or web-based interface, to integrative, distributed and extensible bioinformatics workflow management systems.
Bioinformatics workflow management systems
A bioinformatics workflow management system is a specialized form of a workflow management system A workflow management system (WfMS or WFMS) provides an infrastructure for the set-up, performance and monitoring of a defined sequence of tasks, arranged as a workflow application.
International standards
There are several international standards ...
designed specifically to compose and execute a series of computational or data manipulation steps, or a workflow, in a Bioinformatics application. Such systems are designed to
* provide an easy-to-use environment for individual application scientists themselves to create their own workflows,
* provide interactive tools for the scientists enabling them to execute their workflows and view their results in real-time,
* simplify the process of sharing and reusing workflows between the scientists, and
* enable scientists to track the provenance
Provenance (from the French ''provenir'', 'to come from/forth') is the chronology of the ownership, custody or location of a historical object. The term was originally mostly used in relation to works of art but is now used in similar senses i ...
of the workflow execution results and the workflow creation steps.
Some of the platforms giving this service: Galaxy
A galaxy is a system of stars, stellar remnants, interstellar gas, dust, dark matter, bound together by gravity. The word is derived from the Greek ' (), literally 'milky', a reference to the Milky Way galaxy that contains the Solar Sys ...
, Kepler
Johannes Kepler (; ; 27 December 1571 – 15 November 1630) was a German astronomer, mathematician, astrologer, natural philosopher and writer on music. He is a key figure in the 17th-century Scientific Revolution, best known for his laws of ...
, Taverna
A taverna (Greek: ταβέρνα) is a small Greek restaurant that serves Greek cuisine. The taverna is an integral part of Greek culture and has become familiar to people from other countries who visit Greece, as well as through the establishm ...
, UGENE, Anduril, HIVE.
BioCompute and BioCompute Objects
In 2014, the US Food and Drug Administration sponsored a conference held at the National Institutes of Health
The National Institutes of Health, commonly referred to as NIH (with each letter pronounced individually), is the primary agency of the United States government
The federal government of the United States (U.S. federal government or U ...
Bethesda Campus to discuss reproducibility in bioinformatics. Over the next three years, a consortium of stakeholders met regularly to discuss what would become BioCompute paradigm. These stakeholders included representatives from government, industry, and academic entities. Session leaders represented numerous branches of the FDA and NIH Institutes and Centers, non-profit entities including the Human Variome Project and the European Federation for Medical Informatics, and research institutions including Stanford
Stanford University, officially Leland Stanford Junior University, is a private research university in Stanford, California. The campus occupies , among the largest in the United States, and enrolls over 17,000 students. Stanford is consider ...
, the New York Genome Center, and the George Washington University
, mottoeng = "God is Our Trust"
, established =
, type = Private federally chartered research university
, academic_affiliations =
, endowment = $2.8 billion (2022)
, presi ...
.
It was decided that the BioCompute paradigm would be in the form of digital 'lab notebooks' which allow for the reproducibility, replication, review, and reuse, of bioinformatics protocols. This was proposed to enable greater continuity within a research group over the course of normal personnel flux while furthering the exchange of ideas between groups. The US FDA funded this work so that information on pipelines would be more transparent and accessible to their regulatory staff.
In 2016, the group reconvened at the NIH in Bethesda and discussed the potential for a BioCompute Object, an instance of the BioCompute paradigm. This work was copied as both a "standard trial use" document and a preprint paper uploaded to bioRxiv. The BioCompute object allows for the JSON-ized record to be shared among employees, collaborators, and regulators.
Education platforms
As well as in-person Masters degree
A master's degree (from Latin ) is an academic degree awarded by universities or colleges upon completion of a course of study demonstrating mastery or a high-order overview of a specific field of study or area of professional practice. courses being taught at many universities, the computational nature of bioinformtics lends it to computer-aided and online learning. Software platforms designed to teach bioinformatics concepts and methods include Rosalind and online courses offered through the Swiss Institute of Bioinformatics
The SIB Swiss Institute of Bioinformatics is an academic not-for-profit foundation which federates bioinformatics activities throughout Switzerland.
The institute was established on 30 March 1998 and its mission is to provide core bioinfor ...
Training Portal. The Canadian Bioinformatics Workshops provides videos and slides from training workshops on their website under a Creative Commons
Creative Commons (CC) is an American non-profit organization and international network devoted to educational access and expanding the range of creative works available for others to build upon legally and to share. The organization has releas ...
license. The 4273π project or 4273pi project also offers open source educational materials for free. The course runs on low cost Raspberry Pi
Raspberry Pi () is a series of small single-board computers (SBCs) developed in the United Kingdom by the Raspberry Pi Foundation in association with Broadcom. The Raspberry Pi project originally leaned towards the promotion of teaching basic ...
computers and has been used to teach adults and school pupils. 4273π is actively developed by a consortium of academics and research staff who have run research level bioinformatics using Raspberry Pi computers and the 4273π operating system.
MOOC
A massive open online course (MOOC ) or an open online course is an online course aimed at unlimited participation and open access via the Web. In addition to traditional course materials, such as filmed lectures, readings, and problem sets, ma ...
platforms also provide online certifications in bioinformatics and related disciplines, including Coursera
Coursera Inc. () is a U.S.-based massive open online course provider founded in 2012 by Stanford University computer science professors Andrew Ng and Daphne Koller. Coursera works with universities and other organizations to offer online cour ...
's Bioinformatics Specialization (UC San Diego
The University of California, San Diego (UC San Diego or colloquially, UCSD) is a public land-grant research university in San Diego, California. Established in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is th ...
) and Genomic Data Science Specialization (Johns Hopkins
Johns Hopkins (May 19, 1795 – December 24, 1873) was an American merchant, investor, and philanthropist. Born on a plantation, he left his home to start a career at the age of 17, and settled in Baltimore, Maryland where he remained for most ...
) as well as EdX's Data Analysis for Life Sciences XSeries ( Harvard).
Conferences
There are several large conferences that are concerned with bioinformatics. Some of the most notable examples are Intelligent Systems for Molecular Biology
Intelligent Systems for Molecular Biology (ISMB) is an annual academic conference on the subjects of bioinformatics and computational biology organised by the International Society for Computational Biology (ISCB). The principal focus of the con ...
(ISMB), European Conference on Computational Biology (ECCB), and Research in Computational Molecular Biology (RECOMB).
See also
References
Further reading
* Sehgal et al. : Structural, phylogenetic and docking studies of D-amino acid oxidase activator(DAOA ), a candidate schizophrenia gene. Theoretical Biology and Medical Modelling 2013 10 :3.
* Raul Ise
The Present-Day Meaning Of The Word Bioinformatics
Global Journal of Advanced Research, 2015
* Achuthsankar S Nai
Computational Biology & Bioinformatics – A gentle Overview
Communications of Computer Society of India, January 2007
* Aluru, Srinivas, ed. ''Handbook of Computational Molecular Biology''. Chapman & Hall/Crc, 2006. (Chapman & Hall/Crc Computer and Information Science Series)
* Baldi, P and Brunak, S, ''Bioinformatics: The Machine Learning Approach'', 2nd edition. MIT Press, 2001.
* Barnes, M.R. and Gray, I.C., eds., ''Bioinformatics for Geneticists'', first edition. Wiley, 2003.
* Baxevanis, A.D. and Ouellette, B.F.F., eds., ''Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins'', third edition. Wiley, 2005.
* Baxevanis, A.D., Petsko, G.A., Stein, L.D., and Stormo, G.D., eds., ''Current Protocols ''Current Protocols'' is a series of laboratory manuals for life scientists. The first title, ''Current Protocols in Molecular Biology'', was established in 1987 by the founding editors Frederick M. Ausubel, Roger Brent, Robert Kingston, David D. M ...
in Bioinformatics''. Wiley, 2007.
* Cristianini, N. and Hahn, M
''Introduction to Computational Genomics''
Cambridge University Press, 2006. ( , )
* Durbin, R., S. Eddy, A. Krogh and G. Mitchison, ''Biological sequence analysis''. Cambridge University Press, 1998.
*
* Keedwell, E., ''Intelligent Bioinformatics: The Application of Artificial Intelligence Techniques to Bioinformatics Problems''. Wiley, 2005.
* Kohane, et al. ''Microarrays for an Integrative Genomics.'' The MIT Press, 2002.
* Lund, O. et al. ''Immunological Bioinformatics.'' The MIT Press, 2005.
* Pachter, Lior and Sturmfels, Bernd. "Algebraic Statistics for Computational Biology" Cambridge University Press, 2005.
* Pevzner, Pavel A. ''Computational Molecular Biology: An Algorithmic Approach'' The MIT Press, 2000.
* Soinov, L
Bioinformatics and Pattern Recognition Come Together
Journal of Pattern Recognition Research
JPRR
, Vol 1 (1) 2006 p. 37–41
* Stevens, Hallam, ''Life Out of Sequence: A Data-Driven History of Bioinformatics'', Chicago: The University of Chicago Press, 2013,
* Tisdall, James. "Beginning Perl for Bioinformatics" O'Reilly, 2001.
* ttp://www.nap.edu/catalog/2121.html Calculating the Secrets of Life: Contributions of the Mathematical Sciences and computing to Molecular Biology (1995)
Foundations of Computational and Systems Biology MIT Course
Computational Biology: Genomes, Networks, Evolution Free MIT Course
External links
*
*
*
Bioinformatics Resource Portal (SIB)
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