<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>Are you getting gene fusions or just more exons? Gene fusions can be reduced by setting correct_est_fusion=1, or reducing pred_flank, although reducing pred_flank can cause other issues (but those generally only appear if setting the value below below 150). Also if you have the maximum intron size set to high (split_hit option), you may also be generating bridging alignments that make evidence align across distant paralogous genes as well (this can result in gene merging)</div><div><br></div><div>You should also look at your results manually in a viewer like Apollo. Then see if the extra exons are supported by something such as protein alignments from another species. If this is the case, you may have a poorly annotated protein set that is being used as evidence that is carrying over it's erroneous exons into the species you are annotating. If the extra exons are supported by EST evidence, then perhaps you should try and rebuild the EST assembly (for example trinity has an option to use a Jarccardian similarity coefficient to avoid fusing transcripts).</div><div><br></div><div>Another option, is to retrain SNAP or Augustus. MAKER does not actually produce any of the models itself (it is a pipeline not a predictor). The models are all generated using these other algorithms, MAKER just feeds them hints based on protein and transcript alignments, so making sure training is sufficient is important for those programs to produce their best models.</div><div><br></div><div>Finally make sure your repeat database is sufficient, you may need to generate a species specific repeat library using something like RepeatModeler. Repeats can end up being included as extra exons in gene models because they may contain reading frames the do code for proteins (I.e. reverse transcriptases).</div><div><br></div><div>If you have any questions on any of the above, just let us know.</div><div><br></div><div>Thanks,</div><div>Carson</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> Janna Fierst <<a href="mailto:jfierst@uoregon.edu">jfierst@uoregon.edu</a>><br><span style="font-weight:bold">Date: </span> Monday, August 26, 2013 2:54 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] exon/intron boundaries<br></div><div><br></div><div dir="ltr">Hi,<br><br>I am using MAKER 2.28 to annotate a Caenorhabditid worm genome, and the initial results appear fairly good but we seem to be be annotating too many exons for multiple genes. I was wondering which parameters should be tuned to change the threshold for exon/intron boundaries? Thanks for your help -Janna Fierst<br></div>
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