Ncbiblast: Difference between revisions

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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 ===
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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>
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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.
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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 ./blast.sh  
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<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]]
{| cellpadding="0" style="border:1px solid #BBB" bgcolor="#fafeff"
|#!/bin/bash
|-
| cd working_directory
|-
| time /usr/local/ncbiblast/latest/bin/blastall -p blastn -d /db/ncbiblast/latest/nt -i QUERY -o out.QUERY
|}
<br>
{| cellpadding="0" style="border:1px solid #BBB" bgcolor="#fafeff"
| qub queuename  ./blast.sh
|}
-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]]
Line 57: Line 78:
[[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

Revision as of 14:51, 8 January 2013

NCBI Blast

Category: Bioinformatics

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