mirror of
https://github.com/Ponce/slackbuilds
synced 2024-11-24 10:02:29 +01:00
39 lines
1.9 KiB
Text
39 lines
1.9 KiB
Text
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.
|