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 

#!/bin/bash

cd working_directory

time /usr/local/ncbiblast/latest/bin/blastall -p blastn -d /db/ncbiblast/latest/nt -i QUERY -o out.QUERY

qub 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 zcluster

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

System(s)

Unix