<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Thanks, Carson, for the update on this. No need to implement something. I'll keep it simple and translate the collected transcripts using an appropriate translation table.<div><br></div><div>-Bob</div><div><br><div><div>On May 28, 2012, at 8:43 AM, Carson Holt wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div 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>The alternate translation table is not currently an option. It's one of those things that needs to be implemented, but has not been yet. It's also not supported by many of the eukaryotic gene predictors MAKER uses.</div><div><br></div><div>I could probably get something implemented for you to test in two to three weeks though (there are a lot of places where the translation table comes into play). Let me know.</div><div><br></div><div>--Carson</div><div><br></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> Bob Freeman <<a href="mailto:bob_freeman@hms.harvard.edu">bob_freeman@hms.harvard.edu</a>><br><span style="font-weight:bold">Date: </span> Friday, 25 May, 2012 12:23 PM<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] Alternate translation table?<br></div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hello all!<div><br></div><div>Unusual question here: I am running MAKER on a ciliate that uses a non-standard translation table for its translation products. I haven't found an option in the control files that I can change for the for translation of the predicted transcripts. How or where can I go about this?</div><div><br></div><div>Tx,</div><div>Bob</div><div><br><div><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; 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"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: medium; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; 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margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Bob Freeman, Ph.D.</div><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Acorn Worm Informatics, Kirschner lab</div><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Dept of Systems Biology, Alpert 524</div><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Harvard Medical School</div><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">200 Longwood Avenue</div><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Boston, MA 02115</div><div style="font-style: normal; margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">617/432.2294, vox</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 12px/normal Helvetica; min-height: 14px; "><span class="Apple-style-span" style="font-size: medium; "><div><div><div><div><div><div><div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px; "><br><div style="font-style: normal; ">"Sorry I'm late. Oh, God, that sounded insincere. I'm late."</div><div><span class="Apple-tab-span" style="font-style: normal; white-space: pre; "> </span>-- Karen Walker, from<span class="Apple-converted-space"> </span><i>Will and Grace</i></div><div style="font-style: normal; "><br></div></span></font></div></div></div></div></div></div></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline">
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