Bioinformatics is an interdisciplinary field of science that develops methods and software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The subsequent process of analyzing and interpreting data is referred to as computational biology.
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. 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. Sequence alignments are also used for non-biological sequences such as calculating the distance cost between strings in a natural language, or to display financial data.
The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is located in Bethesda, Maryland, and was founded in 1988 through legislation sponsored by US Congressman Claude Pepper.
In bioinformatics, BLAST is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. A BLAST search enables a researcher to compare a subject protein or nucleotide sequence with a library or database of sequences, and identify database sequences that resemble the query sequence above a certain threshold. For example, following the discovery of a previously unknown gene in the mouse, a scientist will typically perform a BLAST search of the human genome to see if humans carry a similar gene; BLAST will identify sequences in the human genome that resemble the mouse gene based on similarity of sequence.
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes.
BioJava is an open-source software project dedicated to provide Java tools to process biological data. BioJava is a set of library functions written in the programming language Java for manipulating sequences, protein structures, file parsers, Common Object Request Broker Architecture (CORBA) interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic programming, and simple statistical routines. BioJava supports a huge range of data, starting from DNA and protein sequences to the level of 3D protein structures. The BioJava libraries are useful for automating many daily and mundane bioinformatics tasks such as to parsing a Protein Data Bank (PDB) file, interacting with Jmol and many more. This application programming interface (API) provides various file parsers, data models and algorithms to facilitate working with the standard data formats and enables rapid application development and analysis.
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.
FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics.
The European Bioinformatics Institute (EMBL-EBI) is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics.
A phylogenetic network is any graph used to visualize evolutionary relationships between nucleotide sequences, genes, chromosomes, genomes, or species. They are employed when reticulation events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved. They differ from phylogenetic trees by the explicit modeling of richly linked networks, by means of the addition of hybrid nodes instead of only tree nodes. Phylogenetic trees are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as SplitsTree, the R-package, phangorn, and, more recently, Dendroscope. A standard format for representing phylogenetic networks is a variant of Newick format which is extended to support networks as well as trees.
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. Although it was initially developed for genomics research, it is largely domain agnostic and is now used as a general bioinformatics workflow management system.
UGENE is computer software for bioinformatics. It works on personal computer operating systems such as Windows, macOS, or Linux. It is released as free and open-source software, under a GNU General Public License (GPL) version 2.
RNA-Seq is a technique that uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also known as transcriptome.
The Variant Call Format (VCF) is a standard text file format used in bioinformatics for storing gene sequence variations. The format was developed in 2010 for the 1000 Genomes Project and has since been used by other large-scale genotyping and DNA sequencing projects. VCF is a common output format for variant calling programs due to its relative simplicity and scalability. Many tools have been developed for editing and manipulating VCF files, including VCFtools, which was released in conjunction with the VCF format in 2011, and BCFtools, which was included as part of SAMtools until being split into an independent package in 2014.
The Sequence Read Archive is a bioinformatics database that provides a public repository for DNA sequencing data, especially the "short reads" generated by high-throughput sequencing, which are typically less than 1,000 base pairs in length. The archive is part of the International Nucleotide Sequence Database Collaboration (INSDC), and run as a collaboration between the NCBI, the European Bioinformatics Institute (EBI), and the DNA Data Bank of Japan (DDBJ).
.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 division.
Sequence Alignment Map (SAM) is a text-based format originally for storing biological sequences aligned to a reference sequence developed by Heng Li and Bob Handsaker et al. It was developed when the 1000 Genomes Project wanted to move away from the MAQ mapper format and decided to design a new format. The overall TAB-delimited flavour of the format came from an earlier format inspired by BLAT’s PSL. The name of SAM came from Gabor Marth from University of Utah, who originally had a format under the same name but with a different syntax more similar to a BLAST output. It is widely used for storing data, such as nucleotide sequences, generated by next generation sequencing technologies, and the standard has been broadened to include unmapped sequences. The format supports short and long reads (up to 128 Mbp) produced by different sequencing platforms and is used to hold mapped data within the Genome Analysis Toolkit (GATK) and across the Broad Institute, the Wellcome Sanger Institute, and throughout the 1000 Genomes Project.
Bloom filters are space-efficient probabilistic data structures used to test whether an element is a part of a set. Bloom filters require much less space than other data structures for representing sets, however the downside of Bloom filters is that there is a false positive rate when querying the data structure. Since multiple elements may have the same hash values for a number of hash functions, then there is a probability that querying for a non-existent element may return a positive if another element with the same hash values has been added to the Bloom filter. Assuming that the hash function has equal probability of selecting any index of the Bloom filter, the false positive rate of querying a Bloom filter is a function of the number of bits, number of hash functions and number of elements of the Bloom filter. This allows the user to manage the risk of a getting a false positive by compromising on the space benefits of the Bloom filter.
