De novo sequence assemblersDe novo sequence assemblers are a type of program that assembles short nucleotide sequences into longer ones without the use of a reference genome. These are most commonly used in bioinformatic studies to assemble genomes or transcriptomes. Two common types of de novo assemblers are greedy algorithm assemblers and De Bruijn graph assemblers.Third-generation sequencingThird-generation sequencing (also known as long-read sequencing) is a class of DNA sequencing methods that have the capability to produce substantially longer reads (ranging from 10 kb to >1 Mb in length) than second generation sequencing, also known as next-generation sequencing methods. These methods emerged in 2008, characterized by technologies such as nanopore sequencing or single-molecule real-time sequencing, and continue to be developed.De novo transcriptome assemblyDe novo transcriptome assembly is the de novo sequence assembly method of creating a transcriptome without the aid of a reference genome. IntroductionAs a result of the development of novel sequencing technologies, the years between 2008 and 2012 saw a large drop in the cost of sequencing. Per megabase and genome, the cost dropped to 1/100,000th and 1/10,000th of the price, respectively.
Shotgun sequencingIn genetics, shotgun sequencing is a method used for sequencing random DNA strands. It is named by analogy with the rapidly expanding, quasi-random shot grouping of a shotgun. The chain-termination method of DNA sequencing ("Sanger sequencing") can only be used for short DNA strands of 100 to 1000 base pairs.
DNA sequencingDNA 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, thymine, cytosine, and guanine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery.
K-merIn bioinformatics, k-mers are substrings of length k {\displaystyle k} contained within a biological sequence. Primarily used within the context of computational genomics and sequence analysis, in which k-mers are composed of nucleotides (i.e. A, T, G, and C), k-mers are capitalized upon to assemble DNA sequences, improve heterologous gene expression, identify species in metagenomic samples, and create attenuated vaccines.Expressed sequence tag
GenomeIn 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 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.
Sequence alignmentIn 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. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.
DNAMolecule that carries genetic informationThe structure of the DNA double helix (type B-DNA). The atoms in the structure are colour-coded by element and the detailed structures of two base pairs are shown in the bottom right.Simplified diagramDeoxyribonucleic acid (pronunciation; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix.
BioinformaticsBioinformatics ( ) is an interdisciplinary field of science that develops computational methods and software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics integrates principles from biology, chemistry, physics, computer science, data science, computer programming, information engineering, mathematics, and statistics to analyze and interpret biological data.
Transcription (biology)Transcription is the process of duplicating 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, composed of nucleotide sequences.
Shotgun sequencingIn genetics, shotgun sequencing is a method used for sequencing random DNA strands. It is named by analogy with the rapidly expanding, quasi-random shot grouping of a shotgun. The chain-termination method of DNA sequencing ("Sanger sequencing") can only be used for short DNA strands of 100 to 1000 base pairs.DNA sequencingDNA 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, thymine, cytosine, and guanine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery.K-merIn bioinformatics, k-mers are substrings of length k {\displaystyle k} contained within a biological sequence. Primarily used within the context of computational genomics and sequence analysis, in which k-mers are composed of nucleotides (i.e. A, T, G, and C), k-mers are capitalized upon to assemble DNA sequences, improve heterologous gene expression, identify species in metagenomic samples, and create attenuated vaccines.Expressed sequence tagGenomeIn 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 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.Sequence alignmentIn 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. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.DNAMolecule that carries genetic informationThe structure of the DNA double helix (type B-DNA). The atoms in the structure are colour-coded by element and the detailed structures of two base pairs are shown in the bottom right.Simplified diagramDeoxyribonucleic acid (pronunciation; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix.BioinformaticsBioinformatics ( ) is an interdisciplinary field of science that develops computational methods and software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics integrates principles from biology, chemistry, physics, computer science, data science, computer programming, information engineering, mathematics, and statistics to analyze and interpret biological data.Transcription (biology)Transcription is the process of duplicating 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, composed of nucleotide sequences.*As an Amazon Associate I earn from qualifying purchases.