GeMoMa as ABINITO PREDICTION or OTHER PREDICTION

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Sisi Yuan

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Jul 15, 2020, 3:22:54 PM7/15/20

to EVidenceModeler-users

Hi!

I am wondering whether the GeMoMa prediction should be ABINTIO PREDICTION or OTHER PREDICTION in the weights.txt. I tried both but the results are quite different.

Thanks!

Sisi

Brian Haas

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Jul 15, 2020, 5:54:58 PM7/15/20

to Sisi Yuan, EVidenceModeler-users

Basically, if the complete gene prediction is derived from a protein alignment, then you would use OTHER_PREDICTION. If it's making predictions based on the genome contig sequence composition, and hence making inferences about both genic and intergenic regions, then use the ABINITIO_PREDICTION.

The OTHER_PREDICTION type was meant to cover those predictions that do not inform intergenic regions, and are of very high quality (low false positive rates).

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