Ncbiblast: Difference between revisions

Revision as of 13:51, 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

@@ Line 11: / Line 11: @@
 .2.26 is the last updated. older versions are also available.
 === Author / Distributor ===
 [http://www.ncbi.nlm.nih.gov NCBI]
 === Description ===
@@ Line 22: / Line 20: @@
 BLAST (Basic Local Alignment Search Tool)
 === Running Program ===
 Also refer to [[submit jobs to queues]]
 blast+ is documented at [[ncbiblast+ (GACRC)]]<br>
@@ Line 32: / Line 28: @@
 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<br> [[rcc batch blast]] - blast large size of data.
@@ Line 44: / Line 38: @@
 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>
--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]]
@@ Line 57: / Line 78: @@
 [[NCBI]] website.
 === Installation ===
 Executable binary code downloaded from [[NCBI Blast]]
-.
 === System(s) ===
 Unix