<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">MAKER uses the is_start_codon method from Bio::Tools::CodonTable to determine if a codon is a valid start codon. Right now I don’t have a way to swap out the codon table. There is a way to do it, but it’s not easy.<div class=""><br class=""></div><div class="">If you edit …/maker/lib/CGL/TranslationMachine.pm line 122, you can set the table id to be another one from the BioPerl docs —> <a href="http://doc.bioperl.org/releases/bioperl-1.6.1/Bio/Tools/CodonTable.html#BEGIN1" class="">http://doc.bioperl.org/releases/bioperl-1.6.1/Bio/Tools/CodonTable.html#BEGIN1</a></div><div class=""><br class=""></div><div class="">Or you can manually add your own codon table. It won’t change the codon usage for aligners like BLAST and Exonerate, but if will allow you to specify another valid start codon.</div><div class=""><br class=""></div><div class="">To do that, edit line 118 to add your own manual codon table my adding another ‘M’ below the position you want to make into a valid start codon.</div><div class=""><br class=""></div><div class=""><font face="Courier" class=""> my $id = $self->add_table(<br class=""> 'Strict',<br class=""> 'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',<br class=""> '-----------------------------------M----------------------------');<br class=""> $self->id($id);</font></div><div class=""><br class=""></div><div class="">I don’t really know which string position goes with which three letter nucleotide code. You might have to reverse engineer that from the BioPerl docs in the link above.</div><div class=""><br class=""></div><div class="">—Carson<br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jul 21, 2015, at 1:10 PM, Shaun Jackman <<a href="mailto:sjackman@gmail.com" class="">sjackman@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="bloop_markdown" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);"><p style="margin: 15px 0px; -webkit-margin-before: 0px;" class="">Hi, Carson.</p><p style="margin: 15px 0px;" class="">I’m working with a plant mitochondrial genome that has a lot of C to U RNA editing. One effect of this editing is that AUG start codons can be created by editing ACG to AUG. Does MAKER have any particular support for cryptic start codons?</p><p style="margin: 15px 0px;" class="">I’m using protein evidence (<code style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(234, 234, 234); margin: 0px 2px; padding: 0px 5px; word-break: normal; word-wrap: normal; -webkit-margin-before: 0px;" class="">protein</code><span class="Apple-converted-space"> </span>and<span class="Apple-converted-space"> </span><code style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(234, 234, 234); margin: 0px 2px; padding: 0px 5px; word-break: normal; word-wrap: normal;" class="">protein2genome</code>), and a number of the protein sequences that I downloaded from Genbank start with a<span class="Apple-converted-space"> </span><code style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(234, 234, 234); margin: 0px 2px; padding: 0px 5px; word-break: normal; word-wrap: normal;" class="">-</code><span class="Apple-converted-space"> </span>character, which indicates a<span class="Apple-converted-space"> </span><code style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(234, 234, 234); margin: 0px 2px; padding: 0px 5px; word-break: normal; word-wrap: normal;" class="">ACG</code><span class="Apple-converted-space"> </span>start codon. It would fantastic if<span class="Apple-converted-space"> </span><code style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(234, 234, 234); margin: 0px 2px; padding: 0px 5px; word-break: normal; word-wrap: normal;" class="">-</code><span class="Apple-converted-space"> </span>were allowed to match either<span class="Apple-converted-space"> </span><code style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(234, 234, 234); margin: 0px 2px; padding: 0px 5px; word-break: normal; word-wrap: normal;" class="">ACG</code><span class="Apple-converted-space"> </span>or<span class="Apple-converted-space"> </span><code style="font-family: Menlo, Consolas, 'Liberation Mono', Courier, monospace; font-size: 10pt; border-top-left-radius: 3px; border-top-right-radius: 3px; border-bottom-right-radius: 3px; border-bottom-left-radius: 3px; background-color: rgb(248, 248, 248); color: inherit; border: 1px solid rgb(234, 234, 234); margin: 0px 2px; padding: 0px 5px; word-break: normal; word-wrap: normal;" class="">ATG</code><span class="Apple-converted-space"> </span>in the genome.</p><p style="margin: 15px 0px;" class="">Cheers,<br style="-webkit-margin-before: 0px;" class="">Shaun</p><div style="margin: 15px 0px;" class=""><br class="webkit-block-placeholder"></div></div><div class="bloop_original_html" style="font-family: Helvetica, Arial; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(254, 254, 254);"><div id="bloop_customfont" style="font-family: Helvetica, Arial; 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