[Seqinr-forum] querying genbank to get the sequence for an accession

[Jean lobry]

Dear Avril,

>
>Thank you so much for your helpful reply.
>

You're welcome!

>That makes a lot of sense, and it's clear to me now.
>
>I think it's a great idea to provide a function where.is.this.acc() that would
>tell the user which database to find a particular accession number in.

OK, I have just commited it for seqinR release 2.0-7 which will be
available very soon on CRAN because we have to correct an error
generated with R 2.11 (schedulded release in april 2010).

If you want to give it a try, the source code is already available
in the svn repository in the link below, you just have to copy/paste
it in your R console.

http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/pkg/R/where.is.this.acc.R?rev=1704&root=seqinr&view=markup

>I am also wondering whether you only store some accession numbers and not
>others in ACNUC?
>For example, the Haemophilus influenzae Rd KW20 genome sequence is stored in
>GenBank with accessions L42023 (the original submission) and NC_000907.
>
>I find that I can find the sequence by typing in R:
>>  library("seqinr")
>>  choosebank("genbank")
>>  query("haemophilus","AC=L42023")
>
>However, it doesn't work for me to type:
>>  query("haemophilus", "NC_000907")
>I get an error message:
>Error in query("haempphilus", "AC=NC_000907") :
>   invalid request:"unknown accession number at (^): \"AC
>
>I'm wondering if the H. influenza genome sequence is only stored in ACNUC with
>just one accession (L42023), or should I also be able to search for accession
>NC_000907 somehow?
>
>Thanks again for your help, I appreciate it very much.
>

Don't want to give an authoritative answer with the server down.
My guess is that there is a single accession number (by definition)
but that the others may be accessible by keyword queries.

Best,

Jean
-- 
Jean R. Lobry            (lobry at biomserv.univ-lyon1.fr)
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I,
43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE
allo  : +33 472 43 27 56     fax    : +33 472 43 13 88
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