ABCC : Application's document Page

BlastN

April, 2002

Blast, Bioinformatics

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

Standard BLASTN uses the BLAST algorithm to compare a query nucleotide sequence 
against a nucleotide sequence database. BLAST uses a heuristic algorithm which 
seeks local as opposed to global alignments and is therefore able to detect 
relationships among sequences which share only isolated regions of similarity. 
Nucleotide-nucleotide searches are not the recommended way to find homologous 
protein coding regions in other organisms. It is better to perform searches at 
the protein level using the BLASTP, BLASTX or TBLASTX  tool. 

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=BlastN
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=BlastN

Bob Stephens
301-8465787
bobs@ncifcrf.gov

Jigui Shan
shanj@ncifcrf.gov

Jigui Shan and Bob Stephens

2002-04-05