Hi Carson and people,<br><span id="result_box" class="" lang="en"><span class="hps">I am working on</span> <span class="hps">structural</span> <span class="hps">annotation</span> <span class="hps">of a filamentous fungus</span><span>, of which there</span> <span class="hps">is little evidence</span> <span class="hps atn"></span><span>as EST</span> <span class="hps">or</span> <span class="hps">Protein</span><span>.</span> <span class="hps">For generate </span></span><span id="result_box" class="" lang="en"><span class="hps">consensus </span></span><span id="result_box" class="" lang="en"><span class="hps">gene </span> <span class="hps">based on</span> <span class="hps">limited evidence</span>s<span class="hps"> to me</span> <span class="hps">I used</span>  <span class="hps">Marker.</span><br>
 <span class="hps">For this I</span> <span class="hps">created</span> <span class="hps">the files</span> <span class="hps">GeneMark</span> <span class="hps">prediction</span><span class="atn">-</span><span>is and</span> <span class="hps">SNAP.</span><br>
 <span class="hps">I</span> <span class="hps">run maker </span><span class="hps">using the</span> <span class="hps">EST</span> of my organims (85)<span class="hps"></span><span class="hps"></span><span class="hps"></span><span>, along with</span> <span class="hps">5700</span> <span class="hps">EST</span> of the closed organims<span class="hps"></span><span>.</span> <span class="hps"></span>I have <span class="hps">made</span> <span class="hps">​​predictions with</span> <span class="hps">Augustus</span><span>,</span> <span class="hps">and</span> <span class="hps">SNAP</span> <span class="hps"></span><span class="hps"></span> <span class="hps">GeneMark, with the training files for my organims, in Maker pipeline</span><span>.</span> <span class="hps">Everything</span> <span class="hps">works fine.</span><br>
 <span class="hps">My problem</span> <span class="hps">is that when</span> <span class="hps">I get</span> <span class="hps">the consensus sequences</span> <span class="hps">of all my</span> <span class="hps">contigs,</span> <span class="hps">fasta_merge</span> <span class="hps">script</span> <span class="hps">(included in</span> <span class="hps">Maker)</span><span>, I get</span> <span class="hps">different</span> <span class="hps">list for each</span> <span class="hps">predictor</span><span>, as well as</span> <span class="hps">when I try to</span> <span class="hps">get the</span> <span class="hps">gff</span> <span class="hps">of all.</span><br>
 <span class="hps">They could</span> <span class="hps">tell me</span> <span class="hps">how I can use</span> <span class="hps">Maker</span> <span class="hps">consensus</span> <span class="hps">for a list</span> <span class="hps">of</span> <span class="hps">genes?</span> <span class="hps">Or I have to</span> <span class="hps">do it</span> <span class="hps">manually?</span> <span class="hps">There is</span> <span class="hps">the possibility that</span> <span class="hps">Maker</span> <span class="hps">evaluates</span> <span class="hps">the accuracy of</span> <span class="hps">each</span> <span class="hps">prediction</span> <span class="hps">and</span> <span class="hps">confirm</span><span>, so</span> <span class="hps">just get</span> <span class="hps">a list of the</span> <span class="hps">different</span> <span class="hps">predictions?</span><br>
<br> <span class="hps">Thank you very much</span><span>.</span></span><br><br clear="all"><br>-- <br>Eduardo Larriba Tornel<br>Universidad de Alicante.<br>Lab. Fitopatología<br>Dept. Ciencias del Mar y Biología Aplicada<br>
Pabellón 13. <br>San Vicente del Raspeig<br>Tel. 96 590 3400 ext 3280<div style="padding:0px;margin-left:0px;margin-top:0px;overflow:hidden;word-wrap:break-word;color:black;font-size:10px;text-align:left;line-height:130%">
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