<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="">You don’t need to worry about redundancy.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Aug 30, 2017, at 8:01 AM, Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com" class="">qwzhang0601@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class="">Dear Carson:<br class=""><br class=""></div>Thank you again for all you valuable suggestions. Now I am generating the species specific repeat library. I wonder whether I need to remove the masked the regions by existing repeatMasker library, before I run repeatModeler? I think there may be some redundancy if I run repeatModeler directly on the genome and then use both existing repeatMasker library and the repeatModeler library to mask the genome. Does it matter, if there is such redundancy?<br class=""><br class=""></div>Thanks<br class=""><br class=""></div>Best<br class=""></div>Quanwei<br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">2017-08-23 14:10 GMT-04:00 Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span>:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class=""><div class=""><span class=""><br class=""><blockquote type="cite" class=""><div class=""><div dir="ltr" class=""><div class=""><div class="">(1) For the predicted unknown (unclassified) repeat sequences (those in Modelerunknown.lib), it mentioned "Sequences in Modelerunknown.lib were searched against a transposase database (derived from <a rel="nofollow" class="m_-3343096424557117677gmail-text m_-3343096424557117677external" href="http://www.repeatmasker.org/" target="_blank">RepeatMaske</a>r) and sequences matching transposase were considered as transposons belonging to the relevant superfamily". <br class=""></div><div class="">I wonder how to do this search. Annotate the "unknown" repeat sequences using the Repeatmaker? Then what to do, if for an "unknown" repeat sequence, only part of the sequence match the known repeat elements.<br class=""></div></div></div></div></blockquote><div class=""><br class=""></div></span><div class="">You can use RepBase match I guess, but I would not be overly worried about classification. MAKER won’t use any classification info you give it.</div><span class=""><div class=""><br class=""></div><br class=""><blockquote type="cite" class=""><div class=""><div dir="ltr" class=""><div class="">(2) To exclude gene fragments, I need map the predicted repeat sequences against a protein database, and then run the package "ProExcluder"<b class="">. </b>Right?<b class=""> </b>I wonder how to get such protein database.<b class=""> </b>Since I am working on a new rodent species, can I use all the rodent proteins from Uniprot (both Swiss-Prot and TrEMBL)?<br class=""></div></div></div></blockquote><div class=""><br class=""></div></span><div class="">Try Swiss-Prot. That is a well curated cross species set.</div><span class=""><div class=""><br class=""></div><br class=""><blockquote type="cite" class=""><div class=""><div dir="ltr" class="">(3) After I generate the species specific repeat library, do I still need to select a model organism for RepBase masking (as shown below). <br class=""><div class=""><br class=""></div><div class="">In the file "maker_opts.ctl"<br class="">#-----Repeat Masking (leave values blank to skip repeat masking)<br class="">model_org=Mammalia #select a model organism for RepBase masking in RepeatMasker<br class="">rmlib=myRepeat.fa #provide an organism specific repeat library in fasta format for RepeatMasker<br class=""></div></div></div></blockquote></span></div><br class=""><div class="">Yes. Supply both.</div><span class="HOEnZb"><font color="#888888" class=""><div class=""><br class=""></div><div class=""><br class=""></div><div class="">—Carson</div></font></span></div></blockquote></div><br class=""></div>
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