<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="">Look at the region. If it’s being suggested by the polished alignment, I somewhat doubt it’s just an insertion because the polished alignment will have valid splice sites. It could be an insertion, but one that perfectly maps around canonical splice sites would be quite the coincidence (because exonerate shouldn't make big gaps to force the alignment). However if it looks more like a forced mapping around non-canonical spice sites (which shouldn’t actually produce protein2genome results) then I might support the idea that it’s an insertion. A 250bp intron or even a 100 bp doesn’t really seem that short to me. The lower range seen in fungi for example (which have very short introns) can get close to about 20bp. I guess it’s possible that the protein evidence you are using contains an intron that isn’t really there, that results in an intron in your job because of protein conservation (i.e. conserved codons contain the falsely used splice site).<div class=""><br class=""></div><div class="">The minimum intron given to exonerate for polishing is 20. It’s hard coded, and you would have to manually edit it.</div><div class=""><br class=""></div><div class="">Line 1534 in maker/lib/GI.pm —> my $min_intron = 20; </div><div class=""><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jul 15, 2015, at 6:36 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 using<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; -webkit-margin-before: 0px;" class="">protein</code><span class="Apple-converted-space"> </span>evidence 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><span class="Apple-converted-space"> </span>alone without<span class="Apple-converted-space"> </span><em class="">ab initio</em><span class="Apple-converted-space"> </span>gene finders to annotate an organellar genome. MAKER annotates 16 introns. 6 introns look real (according to RNAweasel) and are all larger than 900 bp. The other 10 introns are all shorter than 250 bp and multiples of 3 bp. These short introns look like genomic insertions rather than introns to me. Is there a way to specify a minimum intron size to MAKER?</p><p style="margin: 15px 0px;" class="">6 of these short introns do not contain a stop codon, and 4 do contain a stop codon. I suppose these 4 are pseudogenes.</p><p style="margin: 15px 0px;" class="">Thanks,<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; font-size: 13px; margin: 0px;" class=""><br class=""></div><br class=""><div id="bloop_sign_1437006582812233984" class="bloop_sign"><div style="font-family: helvetica, arial; font-size: 13px;" class="">-- <br class=""><a href="http://sjackman.ca/" style="color: rgb(65, 131, 196); background-color: inherit; text-decoration: none;" class="">http://sjackman.ca/</a></div></div></div><div class="bloop_markdown" style="font-family: Helvetica, Arial; 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