[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 16:11:26 EDT 2010


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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