[maker-devel] GFF features from Maker

[Carson Holt]

Hi Panos,

Terms used are governed by the sequence ontology (http://www.sequenceontology.org <http://www.sequenceontology.org/>), 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.

—Carson





> On Feb 12, 2016, at 1:35 AM, Panos Ioannidis <panos.ioannidis at gmail.com> wrote:
> 
> Hi guys,
> 
> I have a few questions regarding annotated features in the GFF file built by Maker.
> 
> 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?
> 
> 2) Same goes for "protein2genome" and "blastx", since they both give "protein_match" features.
> 
> 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.
> 
> 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
> 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
> 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
> 
> Thanks,
> Panos
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