<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>Not so much "weight" as much as different evidence types help infer different parts of a gene model. ESTs can be used to infer introns, UTR, and splice sites. Proteins help infer exons and CDS. They become "hints" to the gene predictors for the location of these sub-features. Then if ESTs have matching exons that extend beyond the new model produced by SNAP or Augustus using the hints, then they can be added on directly as UTR.</div><div><br></div><div>That error can happen in the older version 2.10, but should not happen with 2.27. To get rid of it you have to edit several lines of code in maker and BioPerl to remove every mention of <span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; ">SDBM_File. It really doesn't effect anything, as the module in question ends up using DB_File regardless.</span></div><div><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; "><br></span></div><div><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; ">Thanks,</span></div><div><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; ">Carson</span></div><div><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; "><br></span></div><div><span class="Apple-style-span" style="font-family: Tahoma; font-size: 13px; "><br></span></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> Sivaranjani Namasivayam <<a href="mailto:ranjani@uga.edu">ranjani@uga.edu</a>><br><span style="font-weight:bold">Date: </span> Tuesday, 26 February, 2013 11:22 PM<br><span style="font-weight:bold">To: </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> [maker-devel] MAKER prediction- evidence weightage<br></div><div><br></div><div dir="ltr"><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><style id="owaParaStyle" type="text/css">P {margin-top:0;margin-bottom:0;}</style><div ocsi="0" fpstyle="1"><div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi,<br><br>
Does MAKER give more weightage to certain type of evidence than others, that is, does it base its annotation more on EST, protein or ab-initio gene prediction? If so which one and is there a way to alter this.<br><br>
Also, when I run MAKER I see the following in the error/log file<br><br>
Can't locate package SDBM_File for @AnyDBM_File::ISA at /usr/local/perl/5.14.1/l<br>
ib/5.14.1/x86_64-linux-thread-multi/DB_File.pm line 293.<br><br>
Can you please tell me how this impacts the results.<br><br>
Thanks,<br>
Ranjani<br></div></div></div>
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