Supercomputer
Using BLAST
This page describes the explanation of Legacy BLAST which is not currently maintained. We recommend using BLAST+ instead of Legacy BLAST.
This information explains the use of BLAST in the NCBI ToolKit provided by The National Center for Biotechnology Information (NCBI).
Record of Service Updates
- November 26, 2006
This page was created.
Contents
Basic use
BLAST distribution contains the following execution programs.
- blastall
- Execute a BLAST search using one of the BLAST programs from the five listed below:
blastp, blastn, blastx, tblastn, tblastx - blastpgp
- Seach by PSI-BLAST or PHI-BLAST mode.
- bl2seq
- Perform the local alignment of two sequences.
- formatdb
- Convert a sequence database from FASTA file format to the BLAST database.
Main options for the 'blastall' command
- [-p]
- Specify one of the five BLAST programs listed below.
Program Query sequence Database blastn nucleotide sequence nucleotide sequence blastp protein sequence protein sequence tblastn protein sequence nucleotide sequence (compare while translating) blastx nucleotide sequence (compare after translating) protein sequence tblastx nucleotide sequence (compare after translating) nucleotide sequence (compare while translating) - [-d]
- Database name.
- [-i]
- Query sequence file name.
- [-o]
- Output file name. Default: standard output
- [-a]
- Parallel execution number
- <Example>
-
·When executing a BLAST search on a local node, login from the 'ngw node to the computing node using 'qlogin'.
[username@ngw01~]$ qlogin
Your job 25769 ("QLOGIN") has been submitted
waiting for interactive job to be scheduled ...
Your interactive job 25769 has been successfully scheduled.
Establishing /home/geadmin/N1GE/util/qlogin_wrapper session to host ncXXXi ..
. username@ncXXXi's password:
Last login: Wed Jan 28 09:54:59 2009 from gw02i
[username@ncXXX ~]$
[username@ncXXX ~]$ higet -d fasta genbank AB094050 > AB094050.fasta
·When executing blast, first create an '.ncbirc' file in the user home directory.
[username@ncXXX ~]$ cat ~/.ncbirc
[NCBI]
Data=/usr/local/package/ncbi_toolkit/current/data
[BLAST]
BLASTDB=/usr/local/db/blast
[username@ncXXX ~]$ blastall -p blastn -d genbank/gss -i AB094050.fasta -o blast.out -a 4
[username@ncXXX ~]$ less blast.out
BLASTN 2.2.19 [Nov-02-2008]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= gi|24106641|gb|AB094050.1|AB094050 Human enterovirus 71 gene
for capsid protein VP1, partial cds, strain:ON001/Hiroshima/97.
(716 letters)
Database: GenBank GSS - genome survey sequence: GenBank nucleic acid
sequence database Release 169
24,661,287 sequences; 15,958,250,844 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
gb|CL563910.1|CL563910 OB__Ba0026P04.f OB__Ba Oryza brachyantha ... 42 2.2
gb|CC309172.1|CC309172 TAM32-32A22_Sp6.1 TAM32 Gallus gallus gen... 42 2.2
gb|FH663950.1|FH663950 CHO_OF5010xg08f1.ab1 CHO_OF5 Nicotiana ta... 42 2.2
gb|ET695836.1|ET695836 CHO_OF027xc12f1.ab1 CHO_OF Nicotiana taba... 42 2.2
gb|ET580136.1|ET580136 fcg3x.229650l16 C. graminicola genomic se... 42 2.2 gb|CE451514.1|CE451514 tigr-gss-dog-17000319213386 Dog Library C... 40 8.8
gb|CC547136.1|CC547136 CH240_430M14.TARBAC13P2 CHORI-240 Bos tau... 40 8.8
gb|AG549971.1|AG549971 Mus musculus molossinus DNA, clone:MSMg01... 40 8.8
<abbrev>