<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>Match/match_part features are expected. MAKER expects these to be polished (I.e. correctly aligned around splice sites). For example exonerate, BLAT, and cufflinks results will be correct around splice sites and can be used; BLAST results on the other hand will not be correct and should not be used.</div><div><br></div><div>The Gap attribute is used by maker if available, but is not required (Gap describes how to reconstruct an alignment for gaps and mismatches). Otherwise MAKER assumes all positions are matches to the reference.</div><div><br></div><div>Thanks,</div><div>Carson</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> Daniel Standage <<a href="mailto:daniel.standage@gmail.com">daniel.standage@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Thursday, 4 October, 2012 2:52 PM<br><span style="font-weight:bold">To: </span> Maker Mailing List <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Expected format for EST GFF3<br></div><div><br></div>Greetings.<div><br></div><div>I would like to use Maker's <b>est_gff</b> option to include EST evidence from an external GFF3 file. In addition to being a valid, well-formed GFF3 file, what expectations does Maker assume about the contents of this file? Which feature types are expected and/or supported? Thanks!<br clear="all"><br>--<br>Daniel S. Standage<br>Ph.D. Candidate<br>Bioinformatics and Computational Biology Program<br>Department of Genetics, Development, and Cell Biology<br>Iowa State University<br><br></div>
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