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Formatdb
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 It has been replaced by makeblastdb and the NCBI "strongly encourage users to stop using formatdb. formatdb must be used in order to format protein or nucleotide source databases before these databases can be searched by BLAST. The source database may be in either FASTA or ASN.1 format. Although the FASTA format is most often used as input to formatdb, the use of ASN.1 is advantageous for those who are using ASN.1 as the common source for other formats such as the GenBank report. The opposite of operation of formatdb, extracting sequences from a blast formatted database, can be achieved by using the fastacmd program, which comes in the same package. In the BLAST+ version, formatdb has been succeeded by makeblastdb. References {{reflist External linksNCBI BLAST Database Format— a description of the BLAST database format with a sam ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BLAST
Blast or The Blast may refer to: * Explosion, a rapid increase in volume and release of energy in an extreme manner *Detonation, an exothermic front accelerating through a medium that eventually drives a shock front Film * ''Blast'' (1997 film), starring Andrew Divoff * ''Blast'' (2000 film), starring Liesel Matthews * ''Blast'' (2004 film), an action comedy film * ''Blast!'' (1972 film) or ''The Final Comedown'', an American drama * ''BLAST!'' (2008 film), a documentary about the BLAST telescope * '' A Blast'', a 2014 film directed by Syllas Tzoumerkas Magazines * ''Blast'' (magazine), a 1914–15 literary magazine of the Vorticist movement * ''Blast'' (U.S. magazine), a 1933–34 American short-story magazine * ''The Blast'' (magazine), a 1916–17 American anarchist periodical Music * Blast (American band), a hardcore punk band * Blast (Russian band), an indie band * ''Blast'' (album), by Holly Johnson, 1989 * ''The Blast'' (album), by Yuvan Shankar Raja, 1999 * " ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Stephen Altschul
Stephen Frank Altschul (born February 28, 1957) is an American mathematician who has designed algorithms that are used in the field of bioinformatics (the Karlin-Altschul algorithm and its successors). Altschul is the co-author of the BLAST algorithm used for sequence analysis of proteins and nucleotides. Education Altschul graduated summa cum laudeNew York Times: "Weddings; Caroline James, Stephen Altschul" April 17, 1994 from , where he was elected to in [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Warren Gish
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. Education After initially studying physics, Gish obtained an Bachelor of Arts, A.B. degree in Biochemistry from University of California, Berkeley, and completed work for his Doctor of Philosophy, Ph.D. degree in Molecular Biology at the same institution in 1988. Research Gish is primarily known for his contributions to National Center for Biotechnology Information, NCBI BLAST, his creation of the BLAST Network Service and nr (non-redundant) databases, his 1996 release of the original gapped BLAST (WU-BLAST 2.0), and most recently his development and support of AB-BLAST. At Washington University in St. Louis, Gish also led the genome analysis group which annotated all finished human, mouse and rat genome data produced by the University's McDonnell Genome Institute, Gen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Webb Miller
Webb Colby Miller (born 1943) is a professor in the Department of Biology and the Department of Computer Science and Engineering at The Pennsylvania State University. Education Miller attended Whitman College, and received his Ph.D. in mathematics from the University of Washington in 1969. Research and career He joined Penn State in September 1985. Prior to that, he had held a position as permanent staff member at the IBM Thomas J. Watson Research Center and served on the faculty at the University of California, Santa Barbara, and the University of Arizona. He is a fellow of the ISCB (International Society for Computational Biology). Miller has been developing algorithms and software for analyzing DNA sequences and related types of data from molecular genetics. He is one of the authors of BLAST. He also develops methods for aligning long DNA sequences and extracting functional information from them. Webb Miller has made important contributions to the analysis of many vertebrate ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
David Lipman
David J. Lipman is an American biologist who from 1989 to 2017 was the director of the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. NCBI is the home of GenBank, the U.S. node of the International Sequence Database Consortium, and PubMed, one of the most heavily used sites in the world for the search and retrieval of biomedical information. Lipman is one of the original authors of the BLAST sequence alignment program, and a respected figure in bioinformatics. In 2017, he left NCBI and became Chief Science Officer at Impossible Foods. Education Lipman received his undergraduate degree from Brown University and his M.D. in 1980 from the University at Buffalo, The State University of New York Career Lipman was the founding director of the National Center for Biotechnology Information, part of the National Library of Medicine at the U.S. National Institutes of Health. Under his leadership, NCBI grew from fewer than a dozen people to more ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FASTA
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. History The original FASTA program was designed for protein sequence similarity searching. Because of the exponentially expanding genetic information and the limited speed and memory of computers in the 1980s heuristic methods were introduced aligning a query sequence to entire data-bases. FASTA, published in 1987, added the ability to do DNA:DNA searches, translated protein:DNA searches, and also provided a more sophisticated shuffling program for evaluating statistical significance. There are several programs in this package that allow the alignment of protein sequences and DNA sequences. Nowadays, increased computer performance makes it possible to perform searches for local alignment detection in a database using the Smith–Waterman algorithm. FASTA is pronounced "fas ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a part of the National Institutes of Health in the United States) as part of the International Nucleotide Sequence Database Collaboration (INSDC). GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 500,000 formally described species. The database started in 1982 by Walter Goad and Los Alamos National Laboratory. GenBank has become an important database for research in biological fields and has grown in recent years at an exponential rate by doubling roughly every 18 months. Release 250.0, published in June 2022, contained over 17 trillion nucleotide bases in more than 2,45 billion sequences. GenBank is built by direct submissions from individual laboratories, as well as from bulk submis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
