[BioPython] BioPython "location->feature" lookup function for GenBank files?

Owen Solberg solberg at berkeley.edu
Tue Feb 7 00:02:39 EST 2006


Does anyone know if there is a way to look up what features lie within a 
sequence range of a GenBank file, using biopython?  Specifically, I have a 
GenBank record for an entire bacterial genome, and I want to be able to 
ask, "What features, if any, are annotated between bases 110,000 and 
120,000." Or "What gene, if any, includes position 534,213?"  And so on. 
This seems like kind of a 'reverse lookup' since most tools seem geared 
for iterating through features, and then returning the qualifiers for each 
feature.  Am I really going to have to make my own reverse lookup to do 
this?  Haven't other people already written this kind of code?

Thanks in advance for your help!

Owen




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