Extracting CDS information from EMBL

Peter Rice pmr at sanger.ac.uk
Wed Jun 16 11:04:33 EST 1999

m.mitchell at icrf.icnet.uk (Mike Mitchell) writes:

> Are there any tools that can extract a CDS from an EMBL entry?
> By this I mean the sequence data rather than the sequence co-ordinates,
> additionlly can such a tool (if one exists) build a CDS from the exon
> boundaries as described by joins?

We are working on adding sequence features to EMBOSS, which will
include extracting CDS sequences from the EMBL/Genbank feature table
and from GFF (Gene-finding features) files.

This will take a little while yet before release but coding is well
under way. EMBOSS will also be able to save ananlysis results in these
formats, so other tools that can use them will be of interest to us.

The EMBOSS home page is http://www.sanger.ac.uk/Software/EMBOSS/

The GFF home page is http://www.sanger.ac.uk/Software/GFF/

Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr at sanger.ac.uk  | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/

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