Ncbiblast: Difference between revisions
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[ | [http://www.ncbi.nlm.nih.gov NCBI] | ||
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Other Utilities<br> [[rcc batch blast]] - blast large size of data.<br> [[blast parser]] - parse the result of blast. | Other Utilities<br> [[rcc batch blast]] - blast large size of data.<br> [[blast parser]] - parse the result of blast. | ||
[[fasta format cleaner]] - check and clean up input fasta format<br> 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: | |||
<pre>#!/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 | |||
</pre> | |||
-p: program names<br> Nucleotide vs nucleotide search using blastn<br> Nucleotide vs protein search with blastx<br> Protein vs protein search with blastp<br> Protein vs nucleotide search with tblastn<br> Nucleotide vs nucleotide search with tblastx<br> -d: database names, ncbi database nt is for blastn, ncbi database nr is for blastp<br> -i: input file in fasta format<br> -o: the name of you output file<br> -a: number of processors, suggested 2 at rcluster.<br> <br> More details of parameters are at [[here]] | -p: program names<br> Nucleotide vs nucleotide search using blastn<br> Nucleotide vs protein search with blastx<br> Protein vs protein search with blastp<br> Protein vs nucleotide search with tblastn<br> Nucleotide vs nucleotide search with tblastx<br> -d: database names, ncbi database nt is for blastn, ncbi database nr is for blastp<br> -i: input file in fasta format<br> -o: the name of you output file<br> -a: number of processors, suggested 2 at rcluster.<br> <br> More details of parameters are at [[here]] | ||
Revision as of 13:02, 8 January 2013
Software Applications
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 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
.
System(s)
Unix