[maker-devel] SNAP scores and AED scores

[Carson Holt]

No.  Snap genes do not disappear. All SNAP ab initio calls will always be
kept as reference fetters marked snap_masked (for repeat masked genome)
and snap (for unmasked genome).  MAKER then runs SNAP another time where
it feeds hints to SNAP based on EST and protein alignment evidence.  These
hint based models can then compete against the ab initio SNAP models to be
promoted to genes if their AED scores are better.  Fianl models can also
get UTR added based on EST evidence.  That is why you can get models from
MAKER that do not match the original SNAP ab initio calls.

So in summary, all SNAP ab initio models will be in snap_masked.  The
MAKER models will consist of hint based SNAP rerun plus SNAP ab intio
models processed to add UTR.

Thanks,
Carson



On 2/13/14, 3:17 AM, "Masa Roller" <masa at bioinfo.hr> wrote:

>Dear all,
>
>I ran snap2 based gene prediction through maker.
>
>In the resulting gff file, in the source "snap_masked" I can find the
>score in the score column of every snap prediction that did not get
>promoted to a maker gene. This would be the score of how well the
>prediction matches the HMM?
>
>It seems to me that those snap models that are given gene status no
>longer appear as snap_masked source but only as source "maker". Maker
>then removes the score column, instead giving AED and eAED scores (which
>are more about how the model corresponds to the evidence). When viewing
>the maker transcripts and SNAP predictions in a browser, they do not
>match (mostly, maker predictions are longer).
>
>I am interested in the score of individual gene predictions that
>underlined maker gene models. Where could I find that information?
>
>Many thanks!
>
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