<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>When you say "gene-like structures:, are you saying that you are looking for pseudogenes and non-coding genes?</div><div><br></div><div>You can use the trnascan and snoscan options in the maker_opts.ctl file to find some non-coding RNAS. You may just want to leave off all ab initio gene predictors like SNAP and Augustus as those will be looking for canonical coding genes.</div><div><br></div><div>If you first hard mask any coding genes, and then provide ESTs or assembled mRNA-seq and proteins, you may be able to use the exonerate alignments produced to identify potential gene like structures. It might require a little post processing of the resulting GFF3 by you.</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> Anand K S Rao <<a href="mailto:aksrao@ucdavis.edu">aksrao@ucdavis.edu</a>><br><span style="font-weight:bold">Date: </span> Thursday, September 25, 2014 at 10:18 AM<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] Using multiple protein profiles as queries for prediction in intergenic regions?<br></div><div><br></div><div dir="ltr">Greetings!<div><br></div><div>I am exploring the use of MAKER-P. But I need your advice in determining if MAKER-P is the best choice for me.</div><div><br></div><div>In the recent past, I've tried using the AUGUSTUS --profile option which allows for user defined protein profiles to be used as query. </div><div><br></div><div>I am interested in predicted gene-like structures in intergenic regions (I've masked away genic regions as predicted by genome annotation pipeline) - in some orphan legume plant species - so not much in the way of extrinsic / external data in the way of EST, NGS data - let alone extrinsic data that might map to so called intergenic regions i.e. whatever little data there exists, has been already used to predict 'genes'.</div><div><br></div><div>When I tried using --profile option of AUGUSTUS, I was not satisfied with the frequency and magnitude of fusion genes. Additionally, there was no easy way for me to consolidate gene-like structures that varied, but overlapped when using different protein profiles as queries (one profile per Pfam HMM within a 4 member clan).</div><div><br></div><div>Additionally, training all the orphan legume species is not an exciting undertaking... because of time and computing resource requirements.</div><div><br></div><div>All this led me to consider MAKER-P as an option. Based on what I've described above, do you think I should proceed with trying to use MAKER-P for my purposes?</div><div><br></div><div>Thank you, in advance.</div><div><br></div><div>Sincerely,</div><div>Anand<br><div><br></div><div><br clear="all"><div><br></div>-- <br><div dir="ltr"><font size="1" face="arial,helvetica,sans-serif"><span style="color:rgb(102,102,102)">Anand K.S. Rao </span> </font><font size="1" color="#666666" face="arial,helvetica,sans-serif"><font>PhD candidate, </font><a href="http://www-plb.ucdavis.edu/" target="_blank">Plant Biology</a> with a <a href="http://deb.ucdavis.edu/" target="_blank">Designated Emphasis in Biotechnology</a></font><span style="color: rgb(102, 102, 102); font-family: arial, helvetica, sans-serif; font-size: x-small;">, </span><div><span style="color: rgb(102, 102, 102); font-family: arial, helvetica, sans-serif; font-size: x-small;"><a href="http://ucdavis.edu/" target="_blank">UC- Davis</a>, CA - 95616 USA | </span><span style="color: rgb(102, 102, 102); font-family: arial, helvetica, sans-serif; font-size: x-small;"><a href="mailto:aksrao@ucdavis.edu" target="_blank">aksrao@ucdavis.edu</a> | (530) 574-5134 | <a href="http://www.linkedin.com/in/anandksrao" target="_blank">LinkedIn</a></span></div><div><span style="color:rgb(153,153,153);font-size:x-small">_________________________________________________________________________</span></div><div><span style="color:rgb(153,153,153);font-size:x-small"> CTTATTGTTGAACTTOAATGGTGCTAATGA</span><span style="color:rgb(153,153,153);font-size:x-small">TCCTCGTOTCTCCTGAACGT - </span><span style="color:rgb(153,153,153);font-size:x-small">translate THAT!</span><br></div></div></div></div></div>
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