un-blastDB

Peter Rice rice at lionbio.co.uk
Tue Jan 2 14:12:24 EST 2001


Jeroen Raes wrote:
> does anybody know of a method to extract the original multifasta file from
> blastdb files which were created with the formatdb command?
> (x.log,x.nhr,x.nin,x.nsq)

EMBOSS will do most of the job - it will read the blastdb files as
a sequence database, and extract a FASTA formatted file of the sequences
(in various forms of the FASTA format).

It is not exactly the same, so you cannot simply use it in blastall, but
you can reindex if with formatdb and use it.

EMBOSS also has most of the code you would need to recreate a FASTA file
to match the file positions in the blast index files.

EMBOSS is free software, available from
http://www.uk.embnet.org/Software/EMBOSS/

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723







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