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diff --git a/academic/ncbi-blast+/README b/academic/ncbi-blast+/README new file mode 100644 index 0000000000000..359bf55c6f869 --- /dev/null +++ b/academic/ncbi-blast+/README @@ -0,0 +1,39 @@ +BLAST+ Command Line Applications + +The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of +local similarity between sequences. The program compares nucleotide or +protein sequences to sequence databases and calculates the statistical +significance of matches. BLAST can be used to infer functional and +evolutionary relationships between sequences as well as help identify +members of gene families. + +The Basic Local Alignment Search Tool (BLAST) is the most widely used +sequence similarity tool. There are versions of BLAST that compare +protein queries to protein databases, nucleotide queries to nucleotide +databases, as well as versions that translate nucleotide queries or +databases in all six frames and compare to protein databases or queries. +PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting +with a protein query, and then uses that PSSM to perform further +searches. It is also possible to compare a protein or nucleotide query +to a database of PSSM’s. The NCBI supports a BLAST web page (at +blast.ncbi.nlm.nih.gov) as well as a network service. The NCBI also +distributes stand-alone BLAST applications for users who wish to run +BLAST on their own machines or with their own databases. + +BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ +Toolkit. The BLAST+ applications have a number of performance and +feature improvements over the legacy BLAST applications (ncbi-blast). + +Some useful links: + +Help https://www.ncbi.nlm.nih.gov/books/NBK1762/ +Manual https://www.ncbi.nlm.nih.gov/books/NBK279690/ +Downloads ftp://ftp.ncbi.nih.gov/blast/executables/blast+/ +Databases ftp://ftp.ncbi.nlm.nih.gov/blast/db/ +ChangeLog http://www.ncbi.nlm.nih.gov/books/NBK131777 +Reference https://www.ncbi.nlm.nih.gov/pubmed/20003500 + +Citing: +BLAST+: architecture and applications. Camacho C, Coulouris G, Avagyan +V, Ma N, Papadopoulos J, Bealer K, Madden TL. BMC Bioinformatics. 2009 +Dec 15;10:421. doi: 10.1186/1471-2105-10-421. |