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39 lines
1.9 KiB
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39 lines
1.9 KiB
Text
BLAST+ Command Line Applications
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The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of
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local similarity between sequences. The program compares nucleotide or
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protein sequences to sequence databases and calculates the statistical
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significance of matches. BLAST can be used to infer functional and
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evolutionary relationships between sequences as well as help identify
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members of gene families.
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The Basic Local Alignment Search Tool (BLAST) is the most widely used
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sequence similarity tool. There are versions of BLAST that compare
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protein queries to protein databases, nucleotide queries to nucleotide
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databases, as well as versions that translate nucleotide queries or
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databases in all six frames and compare to protein databases or queries.
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PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting
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with a protein query, and then uses that PSSM to perform further
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searches. It is also possible to compare a protein or nucleotide query
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to a database of PSSM’s. The NCBI supports a BLAST web page (at
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blast.ncbi.nlm.nih.gov) as well as a network service. The NCBI also
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distributes stand-alone BLAST applications for users who wish to run
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BLAST on their own machines or with their own databases.
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BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++
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Toolkit. The BLAST+ applications have a number of performance and
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feature improvements over the legacy BLAST applications (ncbi-blast).
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Some useful links:
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Help https://www.ncbi.nlm.nih.gov/books/NBK1762/
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Manual https://www.ncbi.nlm.nih.gov/books/NBK279690/
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Downloads ftp://ftp.ncbi.nih.gov/blast/executables/blast+/
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Databases ftp://ftp.ncbi.nlm.nih.gov/blast/db/
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ChangeLog http://www.ncbi.nlm.nih.gov/books/NBK131777
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Reference https://www.ncbi.nlm.nih.gov/pubmed/20003500
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Citing:
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BLAST+: architecture and applications. Camacho C, Coulouris G, Avagyan
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V, Ma N, Papadopoulos J, Bealer K, Madden TL. BMC Bioinformatics. 2009
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Dec 15;10:421. doi: 10.1186/1471-2105-10-421.
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