On Mon, Feb 15, 2010 at 1:30 PM, Alberto Goldoni <
alberto.goldoni1975@gmail.com> wrote:

> Dear all,
> i have a specific question, if i have a sequence of mRNA with some
> mutations, there is a tool in R that can tell me if the mRNA will
> codify or will transform in "mRNA decay"?


Such a tool does not exists in R.  I would be doubtful that such a tool
exists in general, and if it does, it will be very organism dependent.  Even
though a pathway such as NMD exists in most (higher) organisms, the method
by which it recognizes aberrant transcripts is different between organisms
and - for some organisms - poorly understood (and one could argue that we
still don't understand the recognition process in humans).    And this is
just for the NMD pathway; there are several degradation pathways.

Having said that, having something like an early stop codon introduced by a
mutation probably points towards the transcript being degraded by NMD, but
it is hard to know for sure (here, "early" is particular vague).

You might also need to know the UTRs in addition to the coding sequence.

Kasper

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