<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>With the Target and Gap attribute you get slightly better behavior on filtering when you specify the blast_depth=X parameter in the maker_bopts.ctl file (keeps only X best hits). They will also affect the eAED score since it takes reading frame into account (so no Gap attribute means no assumption of reading frame). Otherwise they are only beneficial for seeing the alignment in a viewer as some viewers can recover the alignment when those values are specified. If you are not using blast_depth or trying to view the alignments in a viewer they don't really do anything. MAKER will just assume perfect match across the specified regions.</div><div><br></div><div>--Carson</div><div><br></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> Saturday, May 31, 2014 at 9:23 AM<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] Precomputed alignments<br></div><div><br></div><div dir="ltr"><div><div>Hello again!<br><br></div>About a year ago I asked about using precomputed alignments with Maker. The thread quickly took a different direction as we tried to track down other issues, and I never got the thread back on its original track.<br><br></div>So, to return to the original question, what exactly is required when providing pre-computed alignments in GFF3 format? For example, does it affect Maker's behavior whether a score is given? The "Target" attribute? The "Gap" attribute?<br><br>Thanks!<br clear="all"><div><div><div><div><div dir="ltr"><br>--<br>Daniel S. Standage<br>Ph.D. Candidate<br>Computational Genome Science Laboratory<br>Indiana University<br></div></div></div></div></div></div>
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