<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="">Hi Quanwei, Running maker on the unmasked genome will probably give you more genes, but won’t be helpful in the end. Maker soft-masks repeats, which prevents blast alignments from being seeded in the masked regions, but still allows them to extend into those regions. This solves the problem missing exons mentioned in the text you sent. There’s an option in the control file to run the ab-inition programs on the unmasked sequence (“unmask”) which is set to false (0) by default. <div class=""><br class=""></div><div class="">Hope this helps, </div><div class="">Daniel Ence<br class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Jul 31, 2017, at 12:42 PM, Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com" class="">qwzhang0601@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div dir="ltr" class=""><div class="">Hello:<br class=""><br class=""></div>We are using the Maker2 pipeline to annotating a new genome. We just read something about the repeat masking from repeatMasker's documents. It suggests to leave low complexity region unmasked and to do gene annotation using both masked and unmasked genome. I wonder what your opinion and suggestions on this? Many thanks<br class=""><div class=""><div class=""><div class=""><br class=""><br class="">The paragraph below is from <a href="http://www.binfo.ncku.edu.tw/RM/webrepeatmaskerhelp.html" class="">http://www.binfo.ncku.edu.tw/RM/webrepeatmaskerhelp.html</a><br class=""><h2 class="">Use in association with gene prediction programs</h2><p class="">
Predicting genes from a masked sequence faces several problems. <span style="color:rgb(0,0,255)" class="">First,
one should not mask low complexity regions</span>, e.g. to avoid masking
trinucleotide repeats in coding regions. But even with only
interspersed repeats masked, gene prediction programs may fail to
identify exons correctly. As mentioned above, sometimes tail ends of
coding regions may have originated from transposable elements. Even if
no coding regions have been masked, splice sites may be compromised;
e.g. the polypyrimidine region that is part of the acceptor splice
site may be contained within a repeat.
<br class=""> <br class="">
Thus, I generally recommend to run a gene prediction program on
unmasked DNA (as well) and compare the predicted genes and exons with
the RepeatMasker output. Some gene prediction program allow you to
force certain exons out of the predictions (e.g. often the old ORFs of
LINE1 elements and endogenous retroviruses are included in
genes). Work is also in progress at several sites to incorporate
RepeatMasker into gene prediction programs, in which cases matches to
repeats are weighted in along with the other parameters used. <br class="">
<br class=""></p><p class="">Best</p><p class="">Quanwei<br class=""></p>
<h2 class=""><br class=""></h2></div></div></div></div>
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