[EMBOSS] getting files in GCG format with annotation

[Peter Rice]

Dear Richard,

On 13/07/2011 21:56, Richard Friedman wrote:
> I am learning to use Emboss after being a long-time GCG user.
> The fetch command in GCG returns a file with the sequence in GCG format
> plus annotation.
>
> In EMBOSS I know how to get just sequence in GCG format with seqret.
> In EMBOSS I also know how to get the sequence plus annotation default
> format.
> What I would like to know is how using EMBOSS to get sequence plus
> annotation in GCG format
> like in GCG.

Hmmm ... by "annotation in GCG format" you mean the EMBL or Uniprot 
entry with gaps in the ". ." feaure records?

The obvious question is why you need GCG format. GCG was not very clever 
in handling the annotation.

You can get the sequence plus annotation in one file with:

seqret -feature somedb:someid outfile.seq -osformat embl (or swiss)

That gives you one file with "sequence plus annotation"... and you can 
use the annotation.

You can also get the whole entry text with entret somedb:someid

Hope that helps - and if not, please do ask again!

Peter Rice
EMBOSS Team