<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>On Sep 5, 2012, at 8:26 PM, Zhou Qi wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear maker users and developers:<br><br>I'm new to maker and trying to use it to annotate a Drosophila genome given protein sequences of its closely related species. I have two questions:<br><br>1. How maker decide which one to keep if one query protein has two similarly best hits in the target genome, e.g., gene duplication?<br></div></blockquote><div><br></div><div>MAKER uses the aligned proteins as evidence to support gene predictions (i.e. from SNAP). If the supporting protein can align within the specified parameters (as defined in maker_bopts.ctl) then all of the valid alignments could be used as evidence for gene predictions at those loci.</div><br><blockquote type="cite"><div><br>2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein?<br><br></div></blockquote><div><br></div><div>I don't know of a way to do this by setting parameters in the MAKER control file - maybe Carson has some idea for you here?</div><div><br></div><div><br></div>B</div><div><br><blockquote type="cite"><div>I looked through the previous threads, one possible way seems to use model_gff and map_forward option combined. I guess people more experienced than me using maker might know other ways?<br><br>Many thanks!<br><br>Qi<br>_______________________________________________<br>maker-devel mailing list<br><a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a><br><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><span class="Apple-style-span" style="font-family: Arial; font-size: 12px; "><div>Barry Moore</div><div>Research Scientist</div><div>Dept. of Human Genetics</div><div>University of Utah</div><div>Salt Lake City, UT 84112</div><div>--------------------------------------------</div><div>(801) 585-3543</div><div><br class="khtml-block-placeholder"></div></span></div><div><br></div></span><br class="Apple-interchange-newline">
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