Initiation Codons: "Predictions" And "Alternative Initiation Codons"

Question

[Pierre Lindenbaum]

A colleague has just found a Human mutated sequence having a Valine (GTG ) as the initiation codon, instead of the very classical Methionine (ATG).

She wonders if this protein could be normally expressed.

I found that Valine could be an "Alternative Initiation Codons" ( see http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG1 ) but I'd like to know if some other ATG in the sequence could be some good candidates for an alternative initiation of the translation.

What is your favorite web server for doing this kind of prediction ?

Thanks,

Pierre

Answer 1

[Larry_Parnell]

I cannot offer a tool to use but a person to contact. You should contact Sarah Calvo (of Vamsi Mootha's group at the Broad Institute). She has looked very deeply into 5'-UTRs and upstream open reading frames. In many genes, there are short ORFs that initiate translation from a sequence distinctly upstream from the true Met1 initiation codon. After seeing Sarah speak on more than one occasion, I feel that she would be able to offer some solid advice on the research question at hand.

Answer 2

[Rm]

Prediction of translation initiation sites in human mRNA sequences with AUG start codon in weak Kozak context: A neural network approach.

Obove one is by one of my former collegues Group.

http://bioinfo.iitk.ac.in/AUGPred/

MetWAMer: eukaryotic translation initiation site prediction.

http://brendelgroup.org/bioinformatics2go/MetWAMer.php

http://dx.doi.org/10.1016/j.bbrc.2004.12.053

TISs-ST: a web server to evaluate polymorphic translation initiation sites and their reflections on the secretory targets.

Review: Alternative translation start sites and hidden coding potential of eukaryotic mRNAs