[BiO BB] reading frame, putative protein

[Tirza Doniger]

Although this would not give you a conclusive answer, you could also check
the amino acid composition of the resulting protein and see how it compares
to the amino acid composition of the rest of the organisms proteome.

Best,
Tirza Doniger

On Fri, Apr 30, 2010 at 4:46 PM, Dr. Christoph Gille <
christoph.gille at charite.de> wrote:

> 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
>
>
>
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Tirza Doniger, M.Sc.
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