NCBI Blast

Category(ies): Bioinformatics

Version: Version:2.2.16,
2.2.13, 2.2.14 are also available

Split big query file with multiple query sequences into multiple small input files and run blastall

altix: running program | Documentation | Installation | System

Running Program:

command shortcut is pointed to 2.2.16
2.2.16 is avaiable at /usr/local/ncbiblast and /usr/local/ncbiblast-2.2.16
2.2.14 is avaiable at /usr/local/ncbiblast-2.2.14
2.2.13 is avaiable at /usr/local/ncbiblast-2.2.13

Search utilities
- bl2seq - given two sequences in FASTA format, find regions of local similarity
- blastall - given sequences in FASTA format, find similar sequences in a BLAST database
- megablast - compare highly similar nucleotide sequences
- blastpgp - create protein profiles with iterative and regular expression BLAST
Sequence manipulation utilities
- fastacmd - retrieve FASTA sequences from BLAST databases
- formatdb - create BLAST databases from FASTA sequences
Advanced utilities
- blastclust - automatic sequence clustering
- blastdb - This document describes the "BLAST" databases available on the NCBI FTP site
- blastftp - This file lists the subdirectories and files found on the NCBI BLAST ftp site (ftp://ftp.ncbi.nlm.nih.gov/blast/). It provides the basic information on file content, and on how the files should be used.
Blast database
- ecoli, est, nr, nt,uniprot, more details at here
- documetns at NCBI Blast Database page

Documentation: NCBI Blast at NCBI web site

Installation:

Excutable binary code downloaded from NCBI Blast
Blast database updates every two month or upon request

System(s): Unix

inQuiry: avaiable at inQuiry

pcluster: Not available on pcluster

rcluster, IOB: running program | Documentation | Installation | System

Running Program: also refer to submit jobs to queue at rcluster,IOB

command shortcut is pointed to 2.2.16
2.2.16 is avaiable at /usr/local/ncbiblast and /usr/local/ncbiblast-2.2.16
2.2.14 is avaiable at /usr/local/ncbiblast-2.2.14
For large size of data, please refer to Bioteam BTblast and RCC batch blast program.

e.x.

bsub -q queueName blastall -p blastn -d /db/ncbiblast-latest/nt -i QUERY -o out.QUERY -a 2

-q: queue names at rcluster, more queue information at here
-p: program names
     Nucleotide vs nucleotide search using blastn
     Nucleotide vs protein search with blastx
     Protein vs protein search with blastp
     Protein vs nucleotide search with tblastn
     Nucleotide vs nucleotide search with tblastx
-d: database names, ncbi database nt is for blastn, ncbi database nr is for blastp
-i: input file in fasta format
-o: the name of you output file
-a: number of processors, suggested 2 at rcluster.
More details of paramenters are at here.

There is several blast parsers available at here

Documentation: Same as altix

Installation: Same as altix

System(s): Unix