[Biojava-l] use NCBISequenceDB without gi AC

CEZARD Timothée cezard at nokad-technology.com
Fri Sep 22 13:10:55 UTC 2006

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.

-----Message d'origine-----
De : Richard Holland [mailto:holland at ebi.ac.uk] 
Envoyé : vendredi 22 septembre 2006 10:41
À : Titi
Cc : biojava-l at lists.open-bio.org
Objet : Re: [Biojava-l] use NCBISequenceDB without gi AC

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.


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
> could use NCBISequenceDB.
> Or any solution to access a single database with all kind of accession
> number.
> any answers are welcome.
> Thanks
> Tim
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