[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 15:13:49 EDT 2010


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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