Perhaps you could help with a reading frame problem: I want to verify or reject the hypothesis that there is a yet unknown putative reading frame in a known coding viral gene.
The translated amino acid sequence does not yield any blast or prosite hits. Question: how can I verify by computational methods, that this could be indeed an additional coding reading frame, resulting in an amino acid sequence for which no similar sequence exist in todays databases. What I would do: I would first check in related sequences that the reading frame is indeed open. Then I could look for irregularities in codon usage resulting from the two overlapping reading frames. Then I might observe absense of base wobbling in the third position due to the other reading frame. What would you suggest? What else could I do? Can you recommend any search for functional sites? All methods based on sequence similarity will fail since there is no similar sequence so far. Many thanks Christoph _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
