[maker-devel] GFF features from Maker

[Panos Ioannidis]

Thanks for all the info Carson!

Panos

On Fri, Feb 12, 2016 at 3:56 PM, Carson Holt <carsonhh at gmail.com> wrote:

> 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
>
> —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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