<div dir="ltr">Thanks for the insight.</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Jul 8, 2013 at 8:55 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>This is because augustus never calls it either without hints or after being given hints by MAKER. This may be because even though the exon has support from ESTs and protein alignments, it breaks the open reading frame (you can check using apollo – just click and drag them into the annotation tier). I did this individually for each of the polished proteins and ESTs, and none have proper open reading frame.</div>
<div><br></div><div>Perhaps the official annotation contains a frame shift or something to make it work (augustus can't do that). Such a thing is not all that uncommon. There are many instances of RefSeq annotations for example where if you cut out the exons and try and translate them, they won't translate. This can happen because the reference sequence changed or is incorrect, and if the annotation was generated from a different assembly, then it just gets mapped as best as possible to the current assembly and the correct protein translation is saved elsewhere in the database (even though manual translation won't directly reproduce it). Genes where this happens make up just under 1% of the human genome (but they can drive you nuts especially if your analysis expects protein sequence to match the nucleotide sequence translation). It's really just an artifacts of the process used to move annotations forward on the humans genome every time they update the assembly.</div>
<div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span> Innocent Onsongo <<a href="mailto:onson001@umn.edu" target="_blank">onson001@umn.edu</a>><br><span style="font-weight:bold">Date: </span> Monday, July 8, 2013 6:12 PM<br>
<span style="font-weight:bold">To: </span> "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span> [maker-devel] Maker not outputting exons with EST and Protein Evidence<br></div><div><div class="h5"><div><br></div><div dir="ltr">Maker Developers, <div><br></div><div>I am testing Maker on a well annotated contig from the encode project and in one of the genes, maker does not output an exon despite HSPs supporting it. I have attached a compressed folder with</div>
<div><br></div><div>ENr122_genes.gff: The validated genes as per encode</div><div>ENr122.gff: Makers output</div><div>maker_opts.ctl: The control file I used</div><div>ENr122_98669-134249.pptx: A power point visually illustrated the exon in question. </div>
<div><br></div><div>I even set the parameters est2genome and protein2genome to 1 but still Maker did not output this exon. </div><div><br></div><div>Is there a good reason Maker does no have this exon in its final model despite the HSPs supporting it? </div>
<div><div><br></div><div>Thanks, </div><div>Getiria</div><div><br></div>-- <br>Getiria Onsongo, Ph.D.<br>Informatics Analyst, Research Informatics Support System<br>Minnesota Supercomputing Institute for Advanced Computational Research<br>
University of Minnesota<br>Minneapolis, MN 55455<br>Phone: <a href="tel:612-624-0532" value="+16126240532" target="_blank">612-624-0532</a>
</div></div></div></div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>Getiria Onsongo, Ph.D.<br>Informatics Analyst, Research Informatics Support System<br>Minnesota Supercomputing Institute for Advanced Computational Research<br>
University of Minnesota<br>Minneapolis, MN 55455<br>Phone: 612-624-0532
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