Ncbiblast: Difference between revisions
No edit summary |
No edit summary |
||
Line 75: | Line 75: | ||
Unix | Unix | ||
Latest revision as of 10:28, 14 February 2013
NCBI Blast
Category: Bioinformatics
Program on
zcluster
Version
2.2.26 is the last updated. older versions are also available.
Author / Distributor
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 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