<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>We can look into it.</div><div><br></div><div>—Carson</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> "Fields, Christopher J" <<a href="mailto:cjfields@illinois.edu">cjfields@illinois.edu</a>><br><span style="font-weight:bold">Date: </span> Thursday, March 13, 2014 at 3:04 PM<br><span style="font-weight:bold">To: </span> Sajeet Haridas <<a href="mailto:sajeet@gmail.com">sajeet@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>, "<<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>> List" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] geneid (or alternative ab initio predictors)<br></div><div><br></div><div><meta http-equiv="Content-Type" content="text/html; charset=Windows-1252"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
That is nice to know; I’ll have to check the masking on this assembly to see if that is the problem (my guess is that it is).
<div><br></div><div>Carson, re: geneid and ‘hints’, it looks as if geneid can take some hints such as BLAST HSPs (as well as other information), in the form of a GFF ‘homology’ file. I assume it could take protein2genome/est2genome as well through the same route.</div><div><br></div><div>chris</div><div><br><div><div>On Mar 10, 2014, at 1:31 PM, Sajeet Haridas <<a href="mailto:sajeet@gmail.com">sajeet@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">One of the problems I have found with genemark is that it does not understand a soft-masked genome. Hence, the self training is incorrect. I have found marked improvement to genemark's prediction by running the training on a hard masked genome.<br><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Mar 10, 2014 at 10:05 AM, 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: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; position: static; z-index: auto;">
Adding a new predictor can take some time. It obviously requires some<br>
coding. It’s usually not too hard just to convert results to GFF3 and<br>
then pass it in. Integrated support is really only beneficial for<br>
predictors that can take “hints” from evidence alignments (for example we<br>
are working on EVM integration right now -<br><a href="http://evidencemodeler.sourceforge.net/" target="_blank">http://evidencemodeler.sourceforge.net</a>). If SNAP and GeneMark give<br>
problems just drop them. GeneMark really doesn’t work very good on<br>
genomes with complex intron/exon structure (and I really wouldn’t use it<br>
for anything but fungi).<br><br>
Make sure you are also giving sufficient protein evidence. Perhaps all<br>
proteins from chicken and pigeon for example. Then you shouldn’t find<br>
loss of any true genes if just using Augustus. Also try not to use gene<br>
count as an indicator of performance. The value is very deceptive,<br>
especially if the genome assembly is fragmented.<br><br>
Thanks,<br>
Carson<br><div class="HOEnZb"><div class="h5"><br><br><br>
On 3/10/14, 8:52 AM, "Fields, Christopher J" <<a href="mailto:cjfields@illinois.edu">cjfields@illinois.edu</a>> wrote:<br><br>
>I have been running MAKER 2.31 using Augustus and SNAP on an avian<br>
>genome. Augustus gives pretty decent gene model predictions based on a<br>
>custom model we have and the hints MAKER provides. However, SNAP seems<br>
>to throw out a ton of false positives; in many cases this appears to<br>
>cause erroneous gene fusions. Leaving out SNAP altogether however leads<br>
>to a marked decrease in # models overall, which is worse. GeneMark had a<br>
>very similar problem (high # false positives) and thus no marked<br>
>improvement, either when using with both Augustus and SNAP or with<br>
>Augustus alone.<br>
><br>
>I have been exploring using geneid<br>
>(<a href="http://genome.crg.es/software/geneid/" target="_blank">http://genome.crg.es/software/geneid/</a>) as an alternative, based on some<br>
>feedback on another project I worked with int he past. This would be<br>
>feed into MAKER using external GFF, but I wanted to see if anyone has<br>
>tried geneid with MAKER first.<br>
><br>
>Finally, how hard would it be to incorporate alternative callers into<br>
>MAKER? For instance, would it be possible to add these like a ‘plugin’?<br>
><br>
>chris<br>
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