[Bioperl-l] trying to save blast hit sequences to fasta file

[Torsten Seemann]

Alicia,

> Hi, thanks for your help and suggestions. I have tried the example code
> of Jay Hannah and it works perfectly. But what I need to save in fasta
> format is the whole sequence in the database that is similar to my query
> sequence.

Unfortunately the hit_string is only that part of the sequence in the
database that was similar enough to your query sequence. The BLAST
report does not have the whole hit sequence in it, only the locally
aligned part. SearchIO can only give you what it can get from the
BLAST report.

You will need to record the IDs of the database sequences you are
interested in, and write extra code to retrieve the WHOLE hit sequence
from your database.

--Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University