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

There is a blast parser available at here

Documentation: Same as altix

Installation: Same as altix

System(s): Unix