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 [[email protected]] Sent: 18 June 2010 15:25 To: Tiwari, Bela Cc: [email protected] 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 -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
