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Evolution of wholly overlapping genes

Chris Brown cmbrown at iastate.edu
Tue Mar 5 21:47:33 EST 1996

Does anyone know if there any automatic way of weighting positions in
nucleotide sequences which code for two proteins in different reading
frames? I would like to consider the two sequences independently. 

I am studying two such genes in a plant luteovirus, barley yellow dwarf
virus. A 17kDa protein is wholly encoded within the coat protein (22kDa)
gene in a different frame for the 40 or so sequences known. Both are
expressed. Although, there is one sequence of a distantly related
alloluteovirus in which the nested 17 kDa ORF has been lost.

I would like to identify conserved amino-acid sequences important for
each protein, and look for evolutionary divergence in the two proteins.
Is a bit of a headache to look at the sequences- if an amino-acid is
conserved in one sequence frame, odds are it will correspond to a
(different) conserved amino-acid in the other. Which sequence is
constrained then, both?  

Most virologists ignore this problem, I wonder why? They do analyses on
each protein as though there sequences were independent.  

Does any-one have any ideas?  


Chris Brown, PhD						Ph   + (515) 294 4319
Plant Pathology Dept					FAX +(515) 294 9420
Iowa State University					cmbrown at iastate.edu
Ames IA 50011

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