#acl ChrisSeidel:read,write,delete,revert All:read

= Notes on using BLAST =

BLAST provides an option for tabular output that is easily parsed. Use the -m 8 option for tabular output, or the -m 9 option to include headers.

{{{
blastall -i input.fa -d /path/to/db.fa -p blastn -m 8
}}}
Assumes that db.fa is in a directory that also has a correctly formatted database. This can be achieved by:

{{{
formatdb -i db.fa -p F
}}}

The fields are:

||1||Query||The query sequence id||
||2||Subject||The matching subject sequence id||
||3||% id|| ||
||4||alignment length|| ||
||5||mistmatches|| ||
||6||gap openings|| ||
||7||q.start|| ||
||8||q.end|| ||
||9||s.start|| ||
||10||s.end|| ||
||11||e-value|| ||
||12||bit score|| ||