[EMBOSS] EMBOSS database queries

[Michael Thon]

On Dec 12, 2007, at 5:20 PM, Peter Rice wrote:

> Michael Thon wrote:
>> Thanks Peter, I got it working.
>> While I'm at it, a couple more questions popped up:
>> 1) do you know if  these indexes compatible with the  
>> Bio::DB::Registry type databases?
>
> No ... well, we could add Bio::DB indices to the things EMBOSS can  
> retrieve, then they would be :-)
>
>> 2) Is there any way to index and search sequence features?
>
> Not at present - but:
>
> 2a. what would you like to search for ...
> 2b. what would you like as the result ...
>  2b.i. if you want features, what do we call them?
>
Actually, I haven't given it much thought.  But, for starters, one  
might want to retrieve proteins containing domain X, or that are  
annotated with interpro term Y.  Perhaps some of this functionality  
could be accomplished though clever use of the key or des fields i.e.  
by putting all the Interpro terms assigned to a protein in the keyword  
field prior to indexing.

One might also want to query a database of genomic DNA and fetch a  
translation of a gene or its spliced CDS.
best
Mike