[BiO BB] reading frame, putative protein

Dr. Christoph Gille christoph.gille at charite.de
Fri Apr 30 09:46:01 EDT 2010

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

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


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