[Bioperl-l] How to store results of searches of translated DNA in SeqFeature::Store database of the original DNA?

Chris Fields cjfields at illinois.edu
Wed Aug 11 16:45:00 EDT 2010


HMMER3 is parsed by Bio::SearchIO now in bioperl-live, and I think there is a generic SearchIO->GFF3 script floating around the intertubes somewheres...

chris

On Aug 11, 2010, at 3:38 PM, Doug wrote:

> Hi Scott,
> 
> Good idea. Would you happen to know of an existing HMMER3 to GFF3
> converter?
> 
> Thanks for your advice,
> -- Doug
> 
> On Aug 11, 4:16 pm, Scott Cain <sc... at scottcain.net> wrote:
>> Hi Doug,
>> 
>> I don't know if any of the things you've thought of would work; I've
>> never tried it.  My inclination would be to express your data in GFF3
>> and use the standard loader.
>> 
>> Scott
>> 
>> 
>> 
>> 
>> 
>> On Wed, Aug 11, 2010 at 4:11 PM, Doug <douglas.h... at gmail.com> wrote:
>>> One possible answer to my own question: Use
>>> Bio::SeqFeature::PositionProxy's? Would this work?
>> 
>>> On Aug 11, 3:13 pm, Doug <douglas.h... at gmail.com> wrote:
>>>> Hi,
>> 
>>>> I am trying to store in a SeqFeature::Store database the results of
>>>> searches of translated DNA. The DB contains the original DNA
>>>> sequences. For instance, I have done HMMER searches of 6-frame
>>>> translations of the sequences stored in the DB. I want to store these
>>>> results "at" their (equivalent) DNA positions, which I can calculate.
>>>> Preferably, I would like to directly store the SeqFeature::Similarity
>>>> objects that I get from parsing these searches. But they are of course
>>>> located on different coordinate systems than the DNA, so I guess I
>>>> can't (or shouldn't) create a SeqFeature (e.g. Generic) at the correct
>>>> DNA position and then store the Similarity's as sub-SeqFeatures.
>> 
>>>> I could just set the Similarity's position to the (calculated) DNA
>>>> coordinates, or alternately make a new SeqFeature and copy in the
>>>> attributes I want. But is there a more elegant solution?
>> 
>>>> Thanks,
>>>> -- Doug
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioper... at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioper... at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                    216-392-3087
>> Ontario Institute for Cancer Research
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioper... at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




More information about the Bioperl-l mailing list