<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>I need to fix that last update tag. I did a point release, because there were a couple of very minor fixes that didn't justify a full release (tRNA naming and a fasta_merge bug for tRNAs - I think three lines total of code). There won't be another major version release for a while because we're working on MAKER-EVM which will be version 3.0 (joint project for full MAKER integration with EVM). So just point releases on 2.31 (which will be the very last version of MAKER2). I'll fix the static link and add an new one for 2.31.3.</div><div><br></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> Shaun Jackman <<a href="mailto:sjackman@gmail.com">sjackman@gmail.com</a>><br><span style="font-weight:bold">Reply-To: </span> Shaun Jackman <<a href="mailto:sjackman@gmail.com">sjackman@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Friday, May 2, 2014 at 2:00 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Mapping gene names<br></div><div><br></div><div dir="ltr"><div class="markdown-here-wrapper" id="markdown-here-wrapper-329976" style=""><p style="margin:1.2em 0px!important">Fantastic. Thanks, Carson. I didn’t realize that there was a point release of MAKER. It’s not announced on the MAKER home page, which still reports <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline">Last Software Update v2.31 (Feb 11, 2014)</code>. Where are point releases announced?</p><p style="margin:1.2em 0px!important">The <a href="http://yandell.topaz.genetics.utah.edu/maker_downloads/static/maker-2.31.tgz">static link for MAKER 2.31</a> reports <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline">403 Forbidden</code>. Is there a new static link for MAKER 2.31.3?</p><p style="margin:1.2em 0px!important">Cheers,<br>Shaun</p></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 2 May 2014 12:50, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif"><div>That should already be fixed in the current 2.31.3 download. I'll also send you the subversion credentials in a separate e-mail.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span><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"><div class=""><span style="font-weight:bold">From: </span> Shaun Jackman <<a href="mailto:sjackman@gmail.com" target="_blank">sjackman@gmail.com</a>><br><span style="font-weight:bold">Reply-To: </span> Shaun Jackman <<a href="mailto:sjackman@gmail.com" target="_blank">sjackman@gmail.com</a>><br></div><span style="font-weight:bold">Date: </span> Friday, May 2, 2014 at 1:40 PM<div class=""><br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Mapping gene names<br></div></div><div><div class="h5"><div><br></div><div dir="ltr"><div><p style="margin:1.2em 0px!important">Hi, Carson. Do you happen to have a patch that I could test out that fixes the naming of the tRNA identified by tRNAscan?</p><p style="margin:1.2em 0px!important">Is the MAKER subversion repository public, and if so, what’s its URL?</p><p style="margin:1.2em 0px!important">Cheers,<br>Shaun</p><p style="margin:1.2em 0px!important">Shaun wrote…</p><blockquote style="margin:1.2em 0px;border-left-width:4px;border-left-style:solid;border-left-color:rgb(221,221,221);padding:0px 1em;color:rgb(119,119,119);quotes:none"><p style="margin:1.2em 0px!important">The integration of MAKER-P with tRNAscan is very useful. The identified genes are named e.g. <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline">trnascan-205522-processed-gene-0.38</code>. tRNA genes are conventionally named according to the amino acid and anticodon, such as <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:pre-wrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline">trnW-CCA</code>. Would it be possible for MAKER to name or perhaps prefix the names with that convention?</p></blockquote><p style="margin:1.2em 0px!important">On 6 March 2014 12:58, Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>> wrote:</p><p style="margin:1.2em 0px!important"></p><div><p></p><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif"><div>Yes. I’ll fix the naming.</div><div><br></div><div>Thanks,</div><div>Carson</div></div></blockquote><p></p></div><p style="margin:1.2em 0px!important"></p></div></div></div></div></span></div></blockquote></div><br></div></span></body></html>