[EMBOSS] getting files in GCG format with annotation

Peter Rice pmr at ebi.ac.uk
Thu Jul 14 16:14:03 UTC 2011

On 14/07/2011 17:08, Richard Friedman wrote:
> 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?

Not necessarily ...

entret reports the exact text of the original input.

seqret -feat with the same format as the input will rewrite everything 
using the output format. If that comes out identical then we are usually 
very happy (we do try to preserve everything in EMBL/GenBank and 
Swissprot formats) but there is no absolute guarantee.

Also, strictly speaking, the output of entret is defined as "text" while 
the output of seqret is defined as "sequence" which leads to some 
distinctions - for example, you cannot choose an alternative output 
format for entret.

Have fun with EMBOSS. Look out for the new release tomorrow!



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