Ncbiblast: Difference between revisions
No edit summary |
|||
| (5 intermediate revisions by the same user not shown) | |||
| Line 5: | Line 5: | ||
=== Program on === | === Program on === | ||
zcluster | zcluster | ||
=== Version === | === Version === | ||
2.2.26 is the last updated. older versions are also available. | 2.2.26 is the last updated. older versions are also available. | ||
=== Author / Distributor === | === Author / Distributor === | ||
[http://www.ncbi.nlm.nih.gov NCBI] | [http://www.ncbi.nlm.nih.gov NCBI] | ||
=== Description === | === Description === | ||
| Line 23: | Line 20: | ||
BLAST (Basic Local Alignment Search Tool) | BLAST (Basic Local Alignment Search Tool) | ||
=== Running Program === | === Running Program === | ||
Also refer to [[submit jobs to queues]] | Also refer to [[submit jobs to queues]] | ||
blast+ is documented at [[ncbiblast+ (GACRC)]]<br> | blast+ is documented at [[ncbiblast+ (GACRC)]]<br> | ||
| Line 33: | Line 28: | ||
mpi blast is documented at [[mpiblast (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+ | Version 1.1 with nabiblast+ is at /usr/local/gpu-blast/1.1-ncbi-blast-2.2.25+ | ||
Other Utilities<br> [[rcc batch blast]] - blast large size of data. | Other Utilities<br> [[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 | [[fasta format cleaner]] - check and clean up input fasta format | ||
/usr/local/ncbiblast/latest/ is pointed to /usr/local/ncbiblast/2.26 | 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: | Example of a shell script blast.sh to run on at the batch queue: | ||
<pre>#!/bin/bash | <pre> | ||
cd working_directory | #!/bin/bash | ||
time /usr/local/ncbiblast/latest/bin/blastall -p blastn -d /db/ncbiblast/latest/nt -i QUERY -o out.QUERY qsub -q queuename | cd working_directory | ||
time /usr/local/ncbiblast/latest/bin/blastall -p blastn -d /db/ncbiblast/latest/nt -i QUERY -o out.QUERY | |||
</pre> | |||
<pre> | |||
qsub -q queuename ./blast.sh | |||
</pre> | </pre> | ||
-p: program names<br> | |||
* 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<br> | |||
-i: input file in fasta format<br> | |||
-o: the name of you output file<br> | |||
-a: number of processors, suggested 2 at zcluster<br> | |||
More details of parameters are at [[here]] | |||
available ncbi databases on zcluster are listed at [[here]] | available ncbi databases on zcluster are listed at [[here]] | ||
=== Documentation === | === Documentation === | ||
[[NCBI]] website. | [[NCBI]] website. | ||
=== Installation === | === Installation === | ||
Executable binary code downloaded from [[NCBI Blast]] | Executable binary code downloaded from [[NCBI Blast]] | ||
=== System(s) === | === System(s) === | ||
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