Ncbiblast

NCBI Blast

Program on

zcluster

Version

2.2.26 is the last updated. older versions are also available.

Author / Distributor

NCBI

Description

BLAST (Basic Local Alignment Search Tool)

Running Program

Also refer to submit jobs to queues

blast+ is documented at ncbiblast+ (GACRC)
gpu blast is documented at gpublast (GACRC)
mpi blast is documented at mpiblast (GACRC)

Version 1.1 with nabiblast+ is at /usr/local/gpu-blast/1.1-ncbi-blast-2.2.25+

Other Utilities
rcc batch blast - blast large size of data.
blast parser - parse the result of blast.

fasta format cleaner - check and clean up input fasta format
Latest version

/usr/local/ncbiblast/latest/ is pointed to /usr/local/ncbiblast/2.26

Example of a shell script blast.sh to run on at the batch queue:

#!/bin/bash
cd working_directory
time /usr/local/ncbiblast/latest/bin/blastall -p blastn -d /db/ncbiblast/latest/nt -i QUERY -o out.QUERY qsub -q queuename  ./blast.sh 

-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 parameters are at here

available ncbi databases on zcluster are listed at here

Documentation

NCBI website.

Installation

Executable binary code downloaded from NCBI Blast

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System(s)

Unix