Difference between revisions of "BLAST+"

Revision as of 22:13, 9 July 2012

In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.

This article focuses on the NCBI "new" BLAST, or blast+ (and starting from version 2.2.26+, released on 3 March 2012).

The latest stable version is: 2.2.26+ (2012-03-03)

see: BLAST for legacy ("old") versions.

Utilities

• Programs contained in blast+ package:

blastdbcheck 

Checks database integrity

blastdbcmd 

Retrieves sequences or other information from a BLAST database

blastdb_aliastool 

Creates database alias

Blastn 

Searches a nucleotide query against a nucleotide database

blastp 

Searches a protein query against a protein database

blastx 

Searches a nucleotide query, dynamically translated in all six frames, against a protein database

blast_formatter 

Formats a web blast result using its assigned request ID (RID)

convert2blastmask 

Converts lowercase masking into makeblastdb readable data

dustmasker 

Masks the low complexity regions in the input nucleotide sequences

legacy_blast.pl 

Converts a legacy blast search command line into blast+ counterpart and execute it

makeblastdb 

Formats input FASTA file(s) into a BLAST database

makembindex 

Indexes an existing nucleotide database for use with megablast

psiblast 

Finds members of a protein family, identifies proteins distantly related to the query, or builds position specific scoring matrix for the query

rpsblast 

Searches a protein against a conserved domain database (CDD) to identify functional domains present in the query

rpstblastn 

Searches a nucleotide query, by dynamically translated it in all six-frames first, against a conserved domain database (CDD)

segmasker 

Masks the low complexity regions in input protein sequences

tblastn 

Searches a protein query against a nucleotide database dynamically translated in all six frames

tblastx 

Searches a nucleotide query, dynamically translated in all six frames, against a nucleotide database similarly translated

update_blastdb.pl 

Downloads preformatted blast databases from NCBI

windowmasker 

Masks repeats found in input nucleotide sequences

Legacy utilities

• Programs contained in the legacy blast package:

bl2seq [1] 

Directly comparing two FASTA sequences

blastall [1] 

legacy blast containing the subfunction of blastn, blastp, blastx, tblastn, and tblastx

blastclust [2] 

Clusters input FASTA sequences into related groups

blastpgp [1] 

Standalone PSI-BLAST for search of distantly related protein sequences and generate position-specific matrices

copymat [2] 

Copies blastpgp output for input to makemat

fastacmd [1] 

Retrieves specific sequence or dumps the sequences from a formatted blast database

formatdb [1] 

Convert FASTA formatted seqeucne file into BLAST database

formatrpsdb [2] 

Format scoremat files into an RPSBLAST database

impala [2] 

protein profile search program, mostly replaced by rpsblast

makemat [2] 

Convert the copymat files into scoremat format, no loger needed by new blastpgp output

megablast [1] 

Faster batch blastn program that uses greedy-algorithm. Works in contiguous or more sensitive discontiguous mode

rpsblast [1] 

reverse PSI-BLAST program for searching against conserved domain database

seedtop [2] 

Pattern search program

Note:

1. Those programs are re-organized into blastn, blastp, blastx, tblastn, tblastx, rpsblast, rpsblastx, psiblast, blastdbcmd and makeblastdb
2. Those programs have no blast+ counterpart at this time.

The commands for legacy blast, comparable to those given for blast+ in section 6, are:

blastall -
fastacmd -d refseq_rna -s nm_000249 -o test_query.fa
blastall -p blastn -i test_query.fa -d refseq_rna -F F -m 9 -b 2 -v 2

External links

• Official website
• BLAST executables — free source downloads
• Standalone BLAST Setup for Unix