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

<p>She wonders if this protein could be normally expressed.</p>

<p>I found that Valine could be an "Alternative Initiation Codons" ( see <a href='http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG1'>http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG1</a> ) 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. </p>

<p>What is your favorite web server for doing this kind of prediction ?</p>

<p>Thanks,</p>

<p>Pierre</p>

<p>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.</p>
