ABCC : Application's document Page

BlastP

April, 2002

Blast, Bioinformatics

Bob Stephens and Jigui Shan
Advanced Biomedical Computing Center(ABCC)

Standard BLASTP uses the BLAST algorithm to compare a query protein sequence 
against a database of protein sequences. Like other BLAST programs, blastp 
algorithm is optimized to find local regions of similarity. However, when 
sequence similarity spans the whole sequence, blastp will report a global 
alignment, which is the preferred result for protein identification purposes.

SunOS, IRIX64, AIX, Linux and OSF1

/abcc/apps/`uname`/ncbi/blastall

for web use:
http://www.abcc.ncifcrf.gov/app/htdocs/appdb/drawpage.php?appname=BlastP
for commandline use:
setenv BLASTDB /abcc/dbase/blastdb/farms
blastall -p blastn -d nr -i QUERY -o out.QUERY
blastall   arguments:
  -p  Program Name [String]
        Input should be one of "blastp", "blastn", "blastx", "tblastn", or "tblastx".
  -d  Database [String]
    default = nr
        The database specified must first be formatted with formatdb.
        Multiple database names (bracketed by quotations) will be accepted.
        An example would be
                -d "nr est"
        which will search both the nr and est databases, presenting the results as if one
        'virtual' database consisting of all the entries from both were searched.   The
        statistics are based on the 'virtual' database of nr and est.
  -i  Query File [File In]
    default = stdin
        The query should be in FASTA format.  If multiple FASTA entries are in the input
        file, all queries will be searched.
  -e  Expectation value (E) [Real]
    default = 10.0
  -o  BLAST report Output File [File Out]  Optional
    default = stdout

http://www.abcc.ncifcrf.gov/app/htdocs/appdb/appinfo.php?appname=BlastP 

Bob Stephens
301-8465787
bobs@ncifcrf.gov

Jigui Shan
shanj@ncifcrf.gov

 Jigui Shan and Bob Stephens

2002-04-12