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EVidenceModeler / EVidenceModeler

source code for EVM
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protein evidence not present in EVM results #35

Open LiuKe98 opened 3 years ago

LiuKe98 commented 3 years ago

Hi everyone,

I used EVM to annote my genome data using ab initio and homology protein alignment. Glancing through the results, I found the gene models that only supported by proteins were discarded. Is it normal?

Thanks a million!

brianjohnhaas commented 3 years ago

Hi,

EVM won't model genes based on protein alignment evidence alone - unless you define high confidence and complete ones as 'OTHER_PREDICTION' evidence types. The alignment data can only be used to supplement internal exons and be combined with ab initio predictions.

best,

~b

On Wed, Nov 4, 2020 at 9:11 PM LiuKe notifications@github.com wrote:

Hi everyone,

I used EVM to annote my genome data using ab initio and homology protein alignment. Glancing through the results, I found the gene models that only supported by proteins were discarded. Is it normal?

Thanks a million!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/EVidenceModeler/EVidenceModeler/issues/35, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKX3NH2NS3MPTBQNUTG3SOICVTANCNFSM4TKYW3OQ .

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

LiuKe98 commented 3 years ago

Dear Brian Haas,

Thanks for your reply. That is really helpful. I know how to do.

All the best

Liuke