<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=""><div class="">Hi Panos,</div><div class=""><br class=""></div>Terms used are governed by the sequence ontology (<a href="http://www.sequenceontology.org" class="">http://www.sequenceontology.org</a>), and specific definitions can be found there. Terms have a Parent/Child relationship with lower levels being more specific than higher levels. The match feature is used for ab initio reference results rather than the potentially better term predicted_gene because match is already handled correctly by most software and most databases like FlyBase already use it for that purpose (in part because predicted_gene was a latecomer to the ontology list and it is used more often to distinguish accepted models without human curation rather than reference predictions). Since match is an experimental_feature, it matches the expected separation between genes (biological_region) and analysis results (experimental_feature). It’s rather boring and technical, but it’s all the result of carful selection using the Sequence Ontology inheritance levels and term definitions. Example in attached image.<div class=""><br class=""></div><div class="">—Carson<br class=""><div class=""><br class=""></div><div class=""><br class=""><div class=""><br class=""></div><div class=""><img alt="SO-0000102.png" apple-inline="yes" id="EED77A65-1258-463F-B84A-C469ABD95EE1" height="576" width="523" apple-width="yes" apple-height="yes" src="cid:3C831C11-2552-4999-BBBB-262F4290B448@hsd1.ut.comcast.net." 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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