[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
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.
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