<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>