From owner-comp-bio@hgmp.mrc.ac.uk Tue Jan 2 19:12:28 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id A6F5717AB9; Tue, 2 Jan 2001 19:12:26 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6023) id 625DD17AB8; Tue, 2 Jan 2001 19:12:24 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 3576F17A70; Tue, 2 Jan 2001 10:01:36 +0000 (GMT) Received: from chi6-1.relay.mail.uu.net (chi6-1.relay.mail.uu.net [199.171.54.98]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 6904F415DF for ; Tue, 2 Jan 2001 10:01:31 +0000 (GMT) Received: from relay1.mail.uk.psi.net by chi6sosrv11.alter.net with ESMTP (peer crosschecked as: relay1.mail.uk.psi.net [154.32.105.6]) id QQjwfg06775 for ; Tue, 2 Jan 2001 10:01:26 GMT Received: from nnrp1.news.uk.psi.net ([154.32.99.130]) by relay1.mail.uk.psi.net with esmtp (Exim 2.12 #2) id 14DOFs-0001iq-00 for bionet-biology-computational@moderators.isc.org; Tue, 2 Jan 2001 10:01:20 +0000 Received: (from news@localhost) by nnrp1.news.uk.psi.net (8.8.5/8.8.5) id KAA20201 for bionet-biology-computational@moderators.isc.org; Tue, 2 Jan 2001 10:01:19 GMT To: bionet-biology-computational@moderators.isc.org Message-ID: <3A51A6EA.E0057DE3@lionbio.co.uk> From: Peter Rice Organization: LION Bioscience Ltd X-Mailer: Mozilla 4.7 [en]C-CCK-MCD (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.biology.computational Subject: Re: un-blastDB References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: 2 Jan 2001 10:01:15 GMT, workstations.lionbio.co.uk Date: Tue, 2 Jan 2001 19:12:24 +0000 (GMT) Sender: owner-comp-bio@hgmp.mrc.ac.uk Precedence: bulk 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@uk.lionbioscience.com +44 1223 224723 .