i'm using command line blast for searching multiple nucleotide queries
against a protein database. For each query I get a detailed output
with hits on the database surviving my cutoff value. There can be a
lot of hits for one single query.
For my task it would be sufficient to know if there is any hit (below
the cutoff) in the database for my query at all. Once the blast search
was able to determine a hit which e-value is lower than my cutoff
value it could print this hit to the output, stop searching and
continue with the next query.
Is some one out there, who can provide me with a simple solution using
custom command line parameters for my blastall binary?
That's my command until now:
/blastall -p blastx -d /path/to/swissprot -e 1e-10 -i input.fas -m 9 >
(using blastall 2.2.15)
Thank you :-)