[Bioperl-l] How to store results of searches of translated DNA in SeqFeature::Store database of the original DNA?
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:
> 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?
> -- Doug
> Bioperl-l mailing list
> Bioper... at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l
More information about the Bioperl-l