[maker-devel] GFF features from Maker

[Panos Ioannidis]

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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