[Biococoa-dev] Reading blast formatted files

Davide Cittaro davide.cittaro at ifom-ieo-campus.it
Fri Aug 11 06:26:47 EDT 2006

On Aug 11, 2006, at 12:18 PM, Koen van der Drift wrote:
> Davide,
> BioCocoa can read fasta files, even with multiple entries.  But  
> maybe blast formatted databases have a different format. Maybe you  
> could point to an example file, so we can see how to implement it?

Actually you can download some blast formatted db from NCBI ftp site  
(ftp://ftp.ncbi.nih.gov/blast/db). They are in binary format and  
indexed, I assume they are some kind of dictionary dumps, so that you  
can retrieve sequences with an accession number. I haven't checked  
NCBI docs and sources, yet :-(


Davide Cittaro
HPC and Bioinformatics Systems @ Informatics Core

IFOM - Istituto FIRC di Oncologia Molecolare
via adamello, 16
20139 Milano

tel.: +39(02)574303355
e-mail: davide.cittaro at ifom-ieo-campus.it

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