[Bioperl-l] SO for RNA-Binding Protein and RNA motifs

[Chris Fields]

Just had a few simple questions about sequence ontology.  What ontology 
terms are being used for RNA-binding proteins (like IRE or TRAP) or 
conserved regulatory RNA motifs such as riboswitches?  I was thinking about 
using TF_binding_site for the former, but is this term mainly for 
DNA-binding proteins?  I found a few terms for conserved elements in SO and 
SOFA (like attenuators), but other conserved motifs (IRE, so on) seem to be 
missing.

I am scanning bacterial genomes for conserved RNA motifs for a few 
different RNA binding proteins and riboswitches and I would like to convert 
this data over to GFF3 to map the positions of the hits to the genomes in 
question.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign