[EMBOSS] getting files in GCG format with annotation

Richard Friedman friedman at cancercenter.columbia.edu
Thu Jul 14 16:08:17 UTC 2011

Dear Peter and Guy,

	I guess I just cling to the familiar. The output formats given by  
emboss are fine,
One more obscure question:

As far as I can see, the output from "seqret -feature" and "entret"  
are the same.
Are there any differences?

Thanks and best wishes,

On Jul 13, 2011, at 5:37 PM, Peter Rice wrote:

> 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
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