[Biopython] BLAST database access

xyz mitlox at op.pl
Tue Jan 26 03:58:53 UTC 2010


Peter wrote:
>> How could I retrieve the sequence which belong to subject id
>> from BLAST database with BioPython?
>>     
>
> Are you using a local BLAST database, or an online one?
> If online, I would try using the hit ID to search via the NCBI
> Entrez interface, see the Bio.Entrez chapter in our tutorial.
> If the database is local, then the NCBI provides a tool as
> part of the BLAST suite for this called fastacmd.
>
> Peter
Thank you. I could retrieve the sequences from a local BlastDB with 
fastacmd, but I have some local BlastDBs which do not have any index,  
because they were created without using the -o T option in formatdb.

How could I retrieve the sequences from local BlastDBs without index?

Thank you in advance.



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