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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 in financial data.
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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.
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.
In molecular biology, open reading frames (ORFs) are defined as spans of DNA sequence between the start and stop codons. Usually, this is considered within a studied region of a prokaryotic DNA sequence, where only one of the six possible reading frames will be "open". Such an ORF may contain a start codon and by definition cannot extend beyond a stop codon. That start codon indicates where translation may start. The transcription termination site is located after the ORF, beyond the translation stop codon. If transcription were to cease before the stop codon, an incomplete protein would be made during translation.
The Smith–Waterman algorithm performs local sequence alignment; that is, for determining similar regions between two strings of nucleic acid sequences or protein sequences. Instead of looking at the entire sequence, the Smith–Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure.
Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations that appear as differing characters in a single alignment column, and insertion or deletion mutations that appear as hyphens in one or more of the sequences in the alignment. Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acids or nucleotides.
T-Coffee is a multiple sequence alignment software using a progressive approach. It generates a library of pairwise alignments to guide the multiple sequence alignment. It can also combine multiple sequences alignments obtained previously and in the latest versions can use structural information from PDB files (3D-Coffee). It has advanced features to evaluate the quality of the alignments and some capacity for identifying occurrence of motifs (Mocca). It produces alignment in the aln format (Clustal) by default, but can also produce PIR, MSF, and FASTA format. The most common input formats are supported.
Sequerome is a web-based sequence profiling tool for integrating the results of a BLAST sequence-alignment report with external research tools and servers that perform advanced sequence manipulations, and allowing the user to record the steps of such an analysis. Sequerome is a web-based Java tool that acts as a front-end to BLAST queries and provides simplified access to web-distributed resources for protein and nucleic acid analysis.
MAVID is a multiple sequence alignment program suitable for the alignment of large numbers of DNA sequences. The sequences can be small mitochondrial genomes or large genomic regions up to megabases long. The latest version is 2.0.4.
In bioinformatics, MAFFT is a program used to create multiple sequence alignments of amino acid or nucleotide sequences. Published in 2002, the first version of MAFFT used an algorithm based on progressive alignment, in which the sequences were clustered with the help of the Fast Fourier Transform. Subsequent versions of MAFFT have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and the addition of new sequences to existing alignments.
MUltiple Sequence Comparison by Log-Expectation (MUSCLE) is computer software for multiple sequence alignment of protein and nucleotide sequences. It is licensed as public domain. The method was published by Robert C. Edgar in two papers in 2004. The first paper, published in Nucleic Acids Research, introduced the sequence alignment algorithm. The second paper, published in BMC Bioinformatics, presented more technical details.
formatdb is a discontinued software tool that was used in molecular bioinformatics to format protein or nucleotide databases for BLAST. It has been replaced by makeblastdb and the NCBI "strongly encourage[s]" users to stop using formatdb.
Warren Richard Gish is the owner of Advanced Biocomputing LLC. He joined Washington University in St. Louis as a junior faculty member in 1994, and was a Research Associate Professor of Genetics from 2002 to 2007.
YASS (Yet Another Similarity Searcher) is a free software, pairwise sequence alignment software for nucleotide sequences, that is, it can search for similarities between DNA or RNA sequences. YASS accepts nucleotide sequences in either plain text or the FASTA format and the output format includes the BLAST tabular output. YASS uses several transition-constrained spaced seed k-mers, which allow considerably improved sensitivity. YASS can be used locally on a user's machine, or as SaaS on the YASS web server, which produces a browser based dot-plot.
FSA is a multiple sequence alignment program for aligning many proteins or RNAs or long genomic DNA sequences. Along with MUSCLE and MAFFT, FSA is one of the few sequence alignment programs which can align datasets of hundreds or thousands of sequences. FSA uses a different optimization criterion which allows it to more reliably identify non-homologous sequences than these other programs, although this increased accuracy comes at the cost of decreased speed.
Phyre and Phyre2 are free web-based services for protein structure prediction. Phyre is among the most popular methods for protein structure prediction having been cited over 1500 times. Like other remote homology recognition techniques, it is able to regularly generate reliable protein models when other widely used methods such as PSI-BLAST cannot. Phyre2 has been designed to ensure a user-friendly interface for users inexpert in protein structure prediction methods. Its development is funded by the Biotechnology and Biological Sciences Research Council.
T-REX is a freely available web server, developed at the department of Computer Science of the Université du Québec à Montréal, dedicated to the inference, validation and visualization of phylogenetic trees and phylogenetic networks. The T-REX web server allows the users to perform several popular methods of phylogenetic analysis as well as some new phylogenetic applications for inferring, drawing and validating phylogenetic trees and networks.
References
- ↑ S. Schwartz, A.; Pachter, L. (19 January 2007). "Multiple alignment by sequence annealing". Bioinformatics. 23 (2): e24–e29. doi:10.1093/bioinformatics/btl311.