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Clear message

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

Blast (last edited 2008-11-18 19:26:06 by ChrisSeidel)