<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Also BLAST vs Exonerate is an algorithmic difference. BLAST aligns using traditional Smith Watmerman resulting in potenially out of order sub alignments called HSPs. Exonerate does spice aware alignments (in order and correctly trimmed for splice sites). More info on polishing alignments on wiki page here —> <a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Polishing_Evidence_Alignments" class="">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Polishing_Evidence_Alignments</a><div class=""><br class=""></div><div class="">—Carson</div><div class=""> <div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Feb 12, 2016, at 1:35 AM, Panos Ioannidis <<a href="mailto:panos.ioannidis@gmail.com" class="">panos.ioannidis@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi guys,<div class=""><br class=""></div><div class="">I have a few questions regarding annotated features in the GFF file built by Maker.</div><div class=""><br class=""></div><div class="">1) I'm a bit confused about the annotations coming from "est2genome" and "blastn", because they both give "expressed_sequence_match" features. So, what's the difference between them? How do the EST matches from est2genome differ from those from blastn?</div><div class=""><br class=""></div><div class="">2) Same goes for "protein2genome" and "blastx", since they both give "protein_match" features.</div><div class=""><br class=""></div><div class="">3) Last, what is the difference between the partial matches and full-length matches? For example, in almost all cases where est2genome gives an "expressed_sequence_match" feature for a genomic area, it also gives a "match_part" feature for sub-areas within this area. What is the meaning of this? I'm pasting one such area, below.</div><div class=""><br class=""></div><div class=""><div class=""><font face="monospace, monospace" class="">scaffold3|size1771164 est2genome expressed_sequence_match 21953 22276 949 + . ID=scaffold3|size1771164:hit:1901:3.2.0.0;Name=C24476_a_3_0_l_241</font></div><div class=""><font face="monospace, monospace" class="">scaffold3|size1771164 est2genome match_part 21953 22035 949 + . ID=scaffold3|size1771164:hsp:1902:3.2.0.0;Parent=scaffold3|size1771164:hit:1901:3.2.0.0;Target=C24476_a_3_0_l_241 1 83 +;Gap=M83</font></div><div class=""><font face="monospace, monospace" class="">scaffold3|size1771164 est2genome match_part 22148 22276 949 + . ID=scaffold3|size1771164:hsp:1903:3.2.0.0;Parent=scaffold3|size1771164:hit:1901:3.2.0.0;Target=C24476_a_3_0_l_241 84 215 +;Gap=M104 D2 M7 I4 M8 I1 M8</font></div></div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Panos</div></div>
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