<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=""><div class="">Currently only 3.0 beta is available. It integrates EVM, and slightly alters some prediction hints for algorithms like Augustus.</div><div class=""><br class=""></div><div class="">It can be used to identify genes on a new reference or update existing gene models (requires that existing models be in GFF3 against the reference genome).</div><div class=""><br class=""></div>I think in the presentation Mark was referring to a separate MAKER fork. The MAKER fork will take a species reference genome, a VCF file derived from resequenced individuals, and it will rebuild gene models around the individual variation. This allows us to identify simple changes like amino acid substitutions between individuals as well as complex changes related to splicing, exon skipping, etc.<div class=""><br class=""></div><div class="">It uses the prediction tool described in this paper (paper contains several examples of variation we can properly predict against) —> <a href="https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btw799/2736367/High-throughput-interpretation-of-gene-structure" class="">https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btw799/2736367/High-throughput-interpretation-of-gene-structure</a></div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Mar 9, 2017, at 2:36 AM, Ole Kristian Tørresen <<a href="mailto:o.k.torresen@ibv.uio.no" class="">o.k.torresen@ibv.uio.no</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi all,<br class="">I was asked to provide some text for a short description of assembly and annotation of a genome, and did some quick googling to see if I was up to date on what has happened with MAKER lately. <br class=""><br class="">First I found the publication from last year describing sequencing and annotation of the desert woodrat (<a href="http://www.sciencedirect.com/science/article/pii/S2213596016300800" class="">http://www.sciencedirect.com/science/article/pii/S2213596016300800</a>). When reading that article, I saw references to MAKER 3.1. As far as I can see from <a href="http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi" class="">http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi</a>, the latest MAKER is 3.00.0-beta. Is 3.1 available somewhere, or is it going to be released soon? <br class=""><br class="">I also saw that a poster that was presented at PAG last year (<a href="https://pag.confex.com/pag/xxiv/webprogram/Paper19035.html" class="">https://pag.confex.com/pag/xxiv/webprogram/Paper19035.html</a>) and was intrigued with the last sentence “...integrating MAKER with resequencing efforts to enable rapid genotype-phenotype association.” Is this part of MAKER 3.1, or a separate effort? I am very interested in the status of this.<br class=""><br class="">Thank you.<br class=""><br class="">Sincerely,<br class="">Ole<br class="">_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br class=""></div></div></blockquote></div><br class=""></div></body></html>