Thank you for your answer. I'm just too lazy I haven't read all the blast documentation. If so, I may have found that set the -I option as true show the GI accession number in the blast output.
Sorry for that. Tim -----Message d'origine----- De : Richard Holland [mailto:[EMAIL PROTECTED] Envoyé : vendredi 22 septembre 2006 10:41 À : Titi Cc : [email protected] Objet : Re: [Biojava-l] use NCBISequenceDB without gi AC -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 The answer is no, unfortunately. There is no way of automatically mapping an accession from one database to another unless the source database provider can give you access to a lookup table containing equivalent pairs of accessions. Whether such things exist, I don't know! It's best if you ask the database providers directly for advice. You should also check your source sequence files that you used to run the blast. You may find that the GI numbers are in the header lines of the FASTA format, in which case you could parse the sequence files to retrieve this information and build your own lookup table. cheers, Richard Titi wrote: > Hello, > > I'm quite new with biojava and need to retrieve Sequence from NCBI. > I've got Blast result containing accession number but this are from their > original database. > for example > dbj|BAC25242.1 > gb|AAQ88642.1 > emb|CAC08176.1 > > Is their any solution to transforme this accession number into gi ones so I > could use NCBISequenceDB. > Or any solution to access a single database with all kind of accession > number. > > any answers are welcome. > > Thanks > > Tim > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFFE6Gh4C5LeMEKA/QRAl66AJsH7MzF6+4x7jY3795pFu295mQ4TgCbB5qf ipqnv/Q8vVYYJmuTSC08HlE= =Rsgd -----END PGP SIGNATURE----- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
