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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG">Hi Carson,<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG"> <o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG">I am Prashant a Bioinformatics postdoctoral fellow from Prof B Venkatesh</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;mso-fareast-language:EN-SG">’s</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG">
lab, IMCB, A*STAR. I am using </span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;mso-fareast-language:EN-SG">MAKER-</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG">tool
to annotate an invertebrate genome (~2Gb). During annotation process, we found several instances of split genes</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;mso-fareast-language:EN-SG"> even though we have full-length reference
protein sequences from very closely related species</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG">. Hence we decided to look at one of the loc</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;mso-fareast-language:EN-SG">i</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG">
to understand the reason behind it and to optimize the parameters.<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG">We
</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;mso-fareast-language:EN-SG">looked at</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG"> a gene ~110kb long
</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;mso-fareast-language:EN-SG">and</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG"> codes for
</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;mso-fareast-language:EN-SG">a
</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG">~1200 amino acid protein. We have a highly identical
</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;mso-fareast-language:EN-SG">reference protein
</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG">(>90% identity and 100% coverage)</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;mso-fareast-language:EN-SG"> from
another species</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG">.
</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;mso-fareast-language:EN-SG">In addition we also have</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG"> a high coverage
</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;mso-fareast-language:EN-SG">Trinity
</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG">transcript assembly
</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;mso-fareast-language:EN-SG">from our species</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG">. Still, this gene
is split into 4 fragments during evidence-based </span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;mso-fareast-language:EN-SG">MAKER</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG">
run. On closer a look, we found that the above mentioned closely related protein is not aligned by exonerate (protein2genome) even though it is the closest protein to this gene in our dataset.
</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;mso-fareast-language:EN-SG">It looks like the program is giving more weightage to transcripts which are typically fragments of the gene. So we are at a loss as to how to predict
this gene in full.</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG">For your reference,
</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;mso-fareast-language:EN-SG">I am herewith enclosing</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG"> maker_opts.ctl
file and maker_bopts.ctl. I will be glad to share the scaffold sequence and other input files if required.<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG">Can you please help me to understand the reason behind MAKER not able to use</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;mso-fareast-language:EN-SG">
the full-length reference</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG"> protein for gene prediction</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black;mso-fareast-language:EN-SG">
and how we can overcome this problem.</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#222222;mso-fareast-language:EN-SG"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">Thanks
<span style="color:black">for your time and help.<o:p></o:p></span></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Best</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif""> regards,<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b><u><span lang="EN-US" style="font-size:9.0pt;color:#0E24F2;mso-fareast-language:EN-SG"><a href="mailto:prashantns@imcb.a-star.edu.sg">Prashant Shingate,
<span style="text-decoration:none">PhD</span></a></span></u></b><b><span lang="EN-US" style="font-size:9.0pt;color:#1F497D;mso-fareast-language:EN-SG">
</span></b><b><span lang="EN-US" style="font-size:9.0pt;color:black;mso-fareast-language:EN-SG">::
</span></b><b><span lang="EN-US" style="font-size:9.0pt;color:#1F497D;mso-fareast-language:EN-SG">Research Fellow :: Comparative and Medical Genomics Lab :: Institute of Molecular and Cell Biology (IMCB) :: Agency for Science, Technology and Research (A*STAR)</span></b><span style="font-size:9.0pt;color:#1F497D;mso-fareast-language:EN-SG"><o:p></o:p></span></p>
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