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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.
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Phyloscan is a web service for DNA sequence analysis that is free and open to all users. For locating matches to a user-specified sequence motif for a regulatory binding site, Phyloscan provides a statistically sensitive scan of user-supplied mixed aligned and unaligned DNA sequence data. Phyloscan's strength is that it brings together
Jun S. Liu is a Chinese-American statistician focusing on Bayesian statistical inference, statistical machine learning, and computational biology. He was Assistant Professor of Statistics at Harvard University from 1991 to 1994. From 1994 to 2004, he was Assistant, Associate, and full Professor of Statistics at Stanford University. Since 2000, Liu has been Professor of Statistics in the Department of Statistics at Harvard University and held a courtesy appointment at Harvard T.H. Chan School of Public Health.
Tandy Warnow is an American computer scientist and Grainger Distinguished Chair in Engineering at the University of Illinois at Urbana–Champaign. She is known for her work on the reconstruction of evolutionary trees, both in biology and in historical linguistics, and also for multiple sequence alignment methods.
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David Sankoff is a Canadian mathematician, bioinformatician, computer scientist and linguist. He holds the Canada Research Chair in Mathematical Genomics in the Mathematics and Statistics Department at the University of Ottawa, and is cross-appointed to the Biology Department and the School of Information Technology and Engineering. He was founding editor of the scientific journal Language Variation and Change (Cambridge) and serves on the editorial boards of a number of bioinformatics, computational biology and linguistics journals. Sankoff is best known for his pioneering contributions in computational linguistics and computational genomics. He is considered to be one of the founders of bioinformatics. In particular, he had a key role in introducing dynamic programming for sequence alignment and other problems in computational biology. In Pavel Pevzner's words, "[ Michael Waterman ] and David Sankoff are responsible for transforming bioinformatics from a ‘stamp collection' of ill-defined problems into a rigorous discipline with important biological applications."
Ron Shamir is an Israeli professor of computer science known for his work in graph theory and in computational biology. He holds the Raymond and Beverly Sackler Chair in Bioinformatics, and is the founder and former head of the Edmond J. Safra Center for Bioinformatics at Tel Aviv University.
Gary Stormo is an American geneticist and currently Joseph Erlanger Professor in the Department of Genetics and the Center for Genome Sciences and Systems Biology at Washington University School of Medicine in St Louis. He is considered one of the pioneers of bioinformatics and genomics. His research combines experimental and computational approaches in order to identify and predict regulatory sequences in DNA and RNA, and their contributions to the regulatory networks that control gene expression.
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References
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- ↑ Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC (1993). "Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment". Science. 262 (5131): 208–214. Bibcode:1993Sci...262..208L. doi:10.1126/science.8211139. PMID 8211139.
- ↑ Gibbs Motif Sampler, Gibbs Motif Sampler, archived from the original on 2011-11-04, retrieved 27 October 2011
- ↑ Sfold, Sfold, archived from the original on 16 September 2011, retrieved 27 October 2011
- ↑ Chip Lawrence Lab, Brown University, retrieved 27 October 2011
- ↑ NCBI, NCBI, retrieved 27 October 2011
