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A BLAST variant called MegaBLAST indexes 4 databases to speed up alignments. [9] BLAT can extend on multiple perfect and near-perfect matches (default is 2 perfect matches of length 11 for nucleotide searches and 3 perfect matches of length 4 for protein searches), while BLAST extends only when one or two matches occur close together. [1] [9]
NCBI has a "Magic-BLAST" tool built around BLAST for this purpose. [31] Comparison When working with genes, BLAST can locate common genes in two related species, and can be used to map annotations from one organism to another. Classifying taxonomy BLAST can use genetic sequences to compare multiple taxa against known taxonomical data.
HPC-BLAST: NCBI compliant multinode and multicore BLAST wrapper. Distributed with the latest version of BLAST, this wrapper facilitates parallelization of the algorithm on modern hybrid architectures with many nodes and many cores within each node. [2] Protein: Burdyshaw CE, Sawyer S, Horton MD, Brook RG, Rekapalli B: 2017 CS-BLAST
The National Center for Biotechnology Information (NCBI) [1] [2] is part of the (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.
Note: BLOSUM 62 is the default matrix for protein BLAST. Experimentation has shown that the BLOSUM-62 matrix is among the best for detecting most weak protein similarities. [1] Several sets of BLOSUM matrices exist using different alignment databases, named with numbers.
NCBI-BLAST, an algorithm for comparing biological sequences from the NCBI; Ensembl, automatic gene annotation by the EMBL-EBI and Sanger Institute; FlyBase is a database of model organism Drosophila melanogaster; GoPubMed is a knowledge-based search engine for biomedical texts; iHOP, information hyperlinked over proteins via gene/protein synonyms
[1] [2] 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. UGENE helps biologists to analyze various biological genetics data, such as sequences , annotations, multiple alignments , phylogenetic trees , NGS ...
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 than 500 scientific staff, and it now hosts hundreds of scientific and medical databases including GenBank, PubMed, PubMed Central, dbGaP, dbSNP, the ...