[maker-devel] GFF features from Maker

[Carson Holt]

Also BLAST vs Exonerate is an algorithmic difference. BLAST aligns using traditional  Smith Watmerman resulting in potenially out of order sub alignments called HSPs. Exonerate does spice aware alignments (in order and correctly trimmed for splice sites). More info on polishing alignments on wiki page here —> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Polishing_Evidence_Alignments <http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Polishing_Evidence_Alignments>

—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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