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.


Basic use

BLAST distribution contains the following execution programs.

Execute a BLAST search using one of the BLAST programs from the five listed below:
blastp, blastn, blastx, tblastn, tblastx
Seach by PSI-BLAST or PHI-BLAST mode.
Perform the local alignment of two sequences.
Convert a sequence database from FASTA file format to the BLAST database.
Main options for the 'blastall' command
Specify one of the five BLAST programs listed below.
ProgramQuery sequenceDatabase
blastnnucleotide sequencenucleotide sequence
blastpprotein sequenceprotein sequence
tblastnprotein sequencenucleotide sequence (compare while translating)
blastxnucleotide sequence (compare after translating)protein sequence
tblastxnucleotide sequence (compare after translating)nucleotide sequence (compare while translating)
Database name.
Query sequence file name.
Output file name. Default: standard output
Parallel execution number
·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

[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


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

Top of Page Top of Page

The University of Tokyo The Institute of Medical Science

Copyright©2005-2019 Human Genome Center