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

Doug douglas.hoen at gmail.com
Wed Aug 11 16:38:54 EDT 2010


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
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> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                    216-392-3087
> Ontario Institute for Cancer Research
>
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