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

[Jay Hannah]

Torsten Seemann wrote:
>> 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.
>   
This probably won't help, but my (extremely poorly documented) 
"SeqLab.net" project

   http://seqlab.net

is a framework that sits on top of BioPerl. The current cross_blast() 
stuff (http://seqlab.net/pods2html/tutorial.html) does this:

   GenBank -> FASTA -> formatdb -> "stand alone" NCBI BLAST -> reports

When the reports run they have simultaneous access to both the original 
Bio::Seq objects from the GenBank file and the Bio::SearchIO objects 
from the BLAST results, so it can kick out reports that understand the 
relationships between (and details of) the original sequences and HSPs 
simultaneously...

If you get stuck trying to do what Torsten suggests and have questions 
about SeqLab.net you could open a ticket with my group

   http://clab.ist.unomaha.edu/CLAB/index.php/RT

and I'll try to help.

Cheers,

Jay Hannah
http://clab.ist.unomaha.edu/CLAB/index.php/User:Jhannah