Extracting CDS information from EMBL

Brian Fristensky frist at cc.umanitoba.ca
Wed Jun 16 12:38:55 EST 1999

Mike Mitchell wrote:
> 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?
> Thanx
> --
> Michael Mitchell                 "Smoke me a kipper,
> User Support                  I'll be back for breakfast."
> Molecular Biology Software      Ace Rimmer, Test Pilot
> +44 (0)171 269 3115                BBC-TV Red Dwarf           ENFJ

If you can work with GenBank files rather than EMBL files,
the FEATURES program in the XYLEM package, as described in

Fristensky, B. (1993) Feature expressions: creating and manipulating
       sequence datasets. Nucleic Acids Research 21:5997-6003.

does what you want. 

Given a file containing one or more sequences in GenBank
format, FEATURES can extract DNA sequence corresponding to
the annotated feature
(eg. CDS, mRNA, exon, intron, promoter...., 3'UTR)
into a new file. Even features that span many GenBank
entries are pulled out automatically.
FEATURES also generates expressions
according to the FEATURES Table 'language'. These
expressions can be modified, or new expressions
written, to pull out more specific sequences.
The XYLEM programs can be run from GDE.
For documentation and screen shots see:


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