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DNA Annotation
In molecular biology and genetics, DNA annotation or genome annotation is the process of describing the structure and function of the components of a genome, by analyzing and interpreting them in order to extract their biological significance and understand the biological processes in which they participate. Among other things, it identifies the locations of genes and all the coding regions in a genome and determines what those genes do. Annotation is performed after a genome is sequenced and assembled, and is a necessary step in genome analysis before the sequence is deposited in a database and described in a published article. Although describing individual genes and their products or functions is sufficient to consider this description as an annotation, the depth of analysis reported in literature for different genomes vary widely, with some reports including additional information that goes beyond a simple annotation. Furthermore, due to the size and complexity of sequenced ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Porphyra Umbilicalis Chloroplast Genome Visualized With Chloroplot
''Porphyra'' is a genus of coldwater seaweeds that grow in cold, shallow seawater. More specifically, it belongs to red algae phylum of laver species (from which comes laverbread), comprising approximately 70 species.Brodie, J.A. and Irvine, L.M. 2003. ''Seaweeds of the British Isles.'' Volume 1 Part 3b. The Natural History Museum, London. It grows in the intertidal zone, typically between the upper intertidal zone and the splash zone in cold waters of temperate oceans. In East Asia, it is used to produce the sea vegetable products ''nori'' (in Japan) and '' gim'' (in Korea). There are considered to be 60–70 species of ''Porphyra'' worldwide Kain, J.M. 1991. Cultivation of attached seaweeds. in Guiry, M.D. and Blunden, G. 1992. ''Seaweed Resources in Europe: Uses and Potential.'' John Wiley and Sons, Chichester and seven around Britain and Ireland, where it has been traditionally used to produce edible sea vegetables on the Irish Sea coast.Hardy, F.G. and Guiry, M.D. 2006. ' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Coding Sequence
The coding region of a gene, also known as the coding DNA sequence (CDS), is the portion of a gene's DNA or RNA that codes for a protein. Studying the length, composition, regulation, splicing, structures, and functions of coding regions compared to non-coding regions over different species and time periods can provide a significant amount of important information regarding gene organization and evolution of prokaryotes and eukaryotes. This can further assist in mapping the human genome and developing gene therapy. Definition Although this term is also sometimes used interchangeably with exon, it is not the exact same thing: the exon can be composed of the coding region as well as the 3' and 5' untranslated regions of the RNA, and so therefore, an exon would be partially made up of coding region. The 3' and 5' untranslated regions of the RNA, which do not code for protein, are termed Non-coding region, non-coding regions and are not discussed on this page. There is often confusi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Non-coding Region
Non-coding DNA (ncDNA) sequences are components of an organism's DNA that do not encode protein sequences. Some non-coding DNA is transcribed into functional non-coding RNA molecules (e.g. transfer RNA, microRNA, piRNA, ribosomal RNA, and regulatory RNAs). Other functional regions of the non-coding DNA fraction include regulatory sequences that control gene expression; scaffold attachment regions; origins of DNA replication; centromeres; and telomeres. Some non-coding regions appear to be mostly nonfunctional, such as introns, pseudogenes, intergenic DNA, and fragments of transposons and viruses. Regions that are completely nonfunctional are called junk DNA. Fraction of non-coding genomic DNA In bacteria, the coding regions typically take up 88% of the genome. The remaining 12% does not encode proteins, but much of it still has biological function through genes where the RNA transcript is functional (non-coding genes) and regulatory sequences, which means that almost all ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Homology
Sequence homology is the homology (biology), biological homology between DNA sequence, DNA, RNA sequence, RNA, or Protein primary structure, 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 speciation event (orthologs), or a Gene duplication, duplication event (paralogs), or else a Horizontal gene transfer, horizontal (or lateral) gene transfer event (xenologs). Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity. Significant similarity is strong evidence that two sequences are related by evolutionary changes from a common ancestral sequence. Sequence alignment, Alignments of multiple sequences are used to indicate which regions of each sequence are homologous. Identity, similarity, and conservation The term "percent homology" is often used to mean "sequence similarity”, that is the percen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 biology, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix (mathematics), matrix. Gaps are inserted between the Residue (chemistry), residues so that identical or similar characters are aligned in successive columns. Sequence alignments are also used for non-biological sequences such as calculating the Edit distance, distance cost between strings in a natural language, or to display financial data. Interpretation If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. In sequence ali ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genome Annotation Timeline
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 genes, other functional regions of the genome such as regulatory sequences (see non-coding DNA), and often a substantial fraction of junk DNA with no evident function. Almost all eukaryotes have mitochondria and a small mitochondrial genome. Algae and plants also contain chloroplasts with a chloroplast genome. The study of the genome is called genomics. The genomes of many organisms have been sequenced and various regions have been annotated. The first genome to be sequenced was that of the virus φX174 in 1977; the first genome sequence of a prokaryote (''Haemophilus influenzae'') was published in 1995; the yeast (''Saccharomyces cerevisiae'') genome was the first eukaryotic genome to be sequenced in 1996. The Human Genome Project was started in October 1990, and the first draft sequences of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Transcription (biology)
Transcription is the process of copying a segment of DNA into RNA for the purpose of gene expression. Some segments of DNA are transcribed into RNA molecules that can encode proteins, called messenger RNA (mRNA). Other segments of DNA are transcribed into RNA molecules called non-coding RNAs (ncRNAs). Both DNA and RNA are nucleic acids, which use base pairs of nucleotides as a Complementarity (molecular biology), complementary language. During transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, Antiparallel (biochemistry), antiparallel RNA strand called a primary transcript. In virology, the term transcription is used when referring to mRNA synthesis from a viral RNA molecule. The genome of many Orthornavirae, RNA viruses is composed of Sense (molecular biology), negative-sense RNA which acts as a template for positive sense viral messenger RNA - a necessary step in the synthesis of viral proteins needed for viral replication. This process ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Markov Model
In probability theory, a Markov model is a stochastic model used to Mathematical model, model pseudo-randomly changing systems. It is assumed that future states depend only on the current state, not on the events that occurred before it (that is, it assumes the Markov property). Generally, this assumption enables reasoning and computation with the model that would otherwise be Intractability (complexity), intractable. For this reason, in the fields of predictive modelling and probabilistic forecasting, it is desirable for a given model to exhibit the Markov property. Introduction Andrey Andreyevich Markov (14 June 1856 – 20 July 1922) was a Russian mathematician best known for his work on stochastic processes. A primary subject of his research later became known as the Markov chain. There are four common Markov models used in different situations, depending on whether every sequential state is observable or not, and whether the system is to be adjusted on the basis of observation ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Haemophilus Influenzae
''Haemophilus influenzae'' (formerly called Pfeiffer's bacillus or ''Bacillus influenzae'') is a Gram-negative, Motility, non-motile, Coccobacillus, coccobacillary, facultative anaerobic organism, facultatively anaerobic, Capnophile, capnophilic pathogenic bacterium of the family Pasteurellaceae. The bacteria are Mesophile, mesophilic and grow best at temperatures between 35 and 37 °C. ''H. influenzae'' was first described in 1893 by Richard Friedrich Johannes Pfeiffer, Richard Pfeiffer during an influenza pandemic when he incorrectly identified it as the causative microbe, which is why the bacteria was given the name "influenzae". ''H. influenzae'' is responsible for a wide range of localized and invasive infections, typically in infants and children, including pneumonia, meningitis, or bloodstream infections. Treatment consists of antibiotics; however, ''H. influenzae'' is often resistant to the penicillin family, but amoxicillin/clavulanic acid can be used in mild cases ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Codon Usage Bias
Codon usage bias refers to differences in the frequency of occurrence of synonymous codons in coding DNA. A codon is a series of three nucleotides (a triplet) that encodes a specific amino acid residue in a polypeptide chain or for the termination of translation (stop codons). There are 64 different codons (61 codons encoding for amino acids and 3 stop codons) but only 20 different translated amino acids. The overabundance in the number of codons allows many amino acids to be encoded by more than one codon. Because of such redundancy it is said that the genetic code is degenerate. The genetic codes of different organisms are often biased towards using one of the several codons that encode the same amino acid over the others—that is, a greater frequency of one will be found than expected by chance. How such biases arise is a much debated area of molecular evolution. Codon usage tables detailing genomic codon usage bias for organisms in GenBank and RefSeq can be found in thHIVE-Co ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ribosome
Ribosomes () are molecular machine, macromolecular machines, found within all cell (biology), cells, that perform Translation (biology), biological protein synthesis (messenger RNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA molecules to form polypeptide chains. Ribosomes consist of two major components: the small and large ribosomal subunits. Each subunit consists of one or more ribosomal RNA molecules and many ribosomal proteins (). The ribosomes and associated molecules are also known as the ''translational apparatus''. Overview The sequence of DNA that encodes the sequence of the amino acids in a protein is transcribed into a messenger RNA (mRNA) chain. Ribosomes bind to the messenger RNA molecules and use the RNA's sequence of nucleotides to determine the sequence of amino acids needed to generate a protein. Amino acids are selected and carried to the ribosome by transfer RNA (tRNA) molecules, which enter the riboso ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
