[EMBOSS] getting organism from accession

[Tiwari, Bela]

Hello, 

Thanks Simon for your suggestion. Being so stuck on seqret, I hadn't thought much about entret. Cheers.

Peter: great news about the new feature for EMBOSS 6.3.0.  

Bela

*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental
Bioinformatics Centre
http://nebc.nerc.ac.uk
tel: 01491 69 2705

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
*************************
________________________________________
From: Peter Rice [pmr at ebi.ac.uk]
Sent: 18 June 2010 15:25
To: Tiwari, Bela
Cc: emboss at lists.open-bio.org
Subject: Re: [EMBOSS] getting organism from accession

On 18/06/2010 13:07, Tiwari, Bela wrote:
> Dear all,
>
> I have a set of accession numbers and I want to retrieve the organism
> that the sequence is associated with - i.e. the content of the OS line
> in an embl file.  I don't need the taxonomic id, and I don't need to
> start traversing taxonomy trees. I want to do this by accessing remote
> databases (via srs, as configured in my emboss.defaults file), rather
> than indexing databases locally.

Coming soon. EMBOSS 6.3.0 will include the capability to pick up the taxid
and to parse the NCBI taxonomy. This opens up a lot of possibilities.

You could also write a little EMBOSS utility to report the Tax string from
the sequence object.

Suggestions for ways to use this information in a future release are welcome.

regards,

Peter
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