<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>It looks like the phase was calculated from the wrong strand orientation. I believe I have corrected this now. I'm checking a few more things, but I'll have 2.28 as the latest release likely tomorrow with the cumulative bug fixes since the last release.</div><div><br></div><div>Thanks,</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> Rob Syme <<a href="mailto:rob.syme@gmail.com">rob.syme@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Tuesday, 21 May, 2013 1:57 AM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Maker-derived CDS GFF3 phase column<br></div><div><br></div><div dir="ltr"><div style="">Hi all</div><div style=""><br></div><div style="">By my reading of the GFF3 spec (<a href="http://sequenceontology.org/resources/gff3.html">http://sequenceontology.org/resources/gff3.html</a>), I'm getting gff3 from Maker that has odd data in the phase column.</div><div style=""><br></div><div style="">For example, see some example Maker output at <a href="https://gist.github.com/robsyme/5617399">https://gist.github.com/robsyme/5617399</a></div><div style=""><br></div><div style="">There are two exons, 5617 <- 5737 and 5793 <- 5953 with phases 0 and 2, respectively. Both exons are in the reverse strand.</div><div style=""><br></div><div style="">From the spec, phase indicates "the number of bases that should be removed from the beginning of this feature to reach the first base of the next codon", and for "reverse strand features, phase is counted from the end field". </div><div style=""><br></div>In the case of the 3' exon (5793 <- 5953), the end field (the 5th column) is 5953. <div>The base at the end field is the first base of the translated CDS, so there should be no bases removed "to reach the first base of the next codon". I suggest that this phase should be 0, not 2.</div><div><br></div><div style="">There is an illustration of the feature at <a href="http://i.imgur.com/DKLxnSf.png">http://i.imgur.com/DKLxnSf.png</a>.</div><div><br></div><div style="">The output gff3 is correct if "the number of bases that should be removed from the beginning of this feature to reach the first base of the next codon" is measured from the 'left-hand' end of this feature (the start field) rather than the end field.</div><div style=""><br></div><div style="">Has anybody else ran into this problem or am I misreading the gff3 spec?</div><div style=""><br></div><div style="">Rob Syme</div><div style="">PhD Student</div><div style="">Curtin University</div><div><br></div><div><br><div style=""><br></div><div style=""><br></div></div></div>
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