Parse Blastdb Format From Java

Question

[Nickengland]

Does anyone know a java library to parse blastDB files? I've found the specification at http://selab.janelia.org/people/farrarm/blastdbfmtv4/blastdbfmt.html for the file format, and the code for a C program to parse it, but not java library. The biojava API doesn't seem to have a class for it either.

Does one exist?

Thanks!

[Pierre Lindenbaum]

just curious: why do you need to parse the internal structure of those DB with java ?

[Nickengland]

I'm doing some sequence mutation analysis from within Java, which uses blast to identify the closest matching genomic sequence. I have ~10million input sequences each run, but only ~200 static sequences in the blastDB to analyse. I could load the fasta files the blastDBs are generated from directly, but that involves mapping which sequences are in which fasta files in the blastDB, as well as needing extra parameters to the program to function (BlastDB and Fasta locations and fasta->sequence mapping) which seems excessive when all that data is in the blastDB file.)