[Bioperl-l] About RNA representations in Bioperl

Christopher Fields cjfields at uiuc.edu
Mon Sep 5 23:51:28 EDT 2005

I am using a few programs to scan genome sequences for potential sites for 
RNA-binding proteins.  I want to get these into GFF format for eventual import 
into a mySQL database for GBrowse in order to map the hits against CDS and 
predicted rho-independent terminators in bacterial genomes.  For the moment, I 
plan on either using 
Bio::SeqFeature::Generic (they are pretty simple matches to sequences, much 
like tRNAscan-SE or BLAST, with start, stop, score, and strand information) or 
creating my own class inheriting from Bio::SeqFeature::Generic.  However, these 
regions are protein-binding regions on RNA, not DNA (much like a ribosome-
binding site).  Should I just use misc_bind or protein_bind as a feature label and 
not worry about it?

I asked a similar question recently, which about what SO term would be 
appropriate.  However, I am trying to start out with a simple approach first and 
then get into the details (like secondary structures, free energies, etc), so any 
information would be helpful (and greatly appreciated).

Chris Fields

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