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 for tabular BLAST output 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 |
|