<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>Using GFF3 pass-through options alone won't allow for the alternate splice prediction to work. You have to also allow gene predictors like SNAP and Augustus to run. MAKER uses mutually exclusive EST data to produce separate hint files in some cases that can produce alternate splice forms from the ab initio predictors. The EST evidence must be very long in general or they will not produce alternate forms. These alternate splice model can then compete against your existing gene models based on scoring statistics MAKER produces and potentially replace them. This may not be what you want though. The alternate splice prediction works better De Novo than for re-annotation.</div><div><br></div><div>The alternate splicing option still needs more work, but I would appreciate any feedback.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Walter Eckalbar <<a href="mailto:weckalba@asu.edu">weckalba@asu.edu</a>><br><span style="font-weight:bold">Date: </span> Monday, 4 June, 2012 1:41 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] question regarding alternate splicing annotation<br></div><div><br></div>Hi Maker developers,<div><br></div><div>I am trying to expand on some current annotations that are already quite good, but only predict protein coding sequence and one isoform per gene, to add UTRs and alternative splice forms from cufflinks data. To do this I put the current annotations in both the model_gff andusing the gff_field, plus the cufflinks gff3 for the ests (as I noticed was suggested in a previous email). I've left everything else as default, except changing alt_splice=1. I am watching the progress of the *.gff.ann files, but I'm not noticing alternate splicing being added, while UTRs are being picked up (exons being added, etc.). This is a vertebrate genome, so run times are fairly long and I just wanted to double check if I wasn't missing something. Will maker go back through a second step to annotate alternative splicing? Or should I be trying something a little different.</div><div><br></div><div>Thanks,</div><div><br></div><div>Walter</div>
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