Maker gene vs snap match in final GFF's

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Maker gene vs snap match in final GFF's

Marcus Naymik
In the final GFF annotations what is the difference between a 'gene' from maker and a 'match' from snap?

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Re: Maker gene vs snap match in final GFF's

Carson Holt-2
MAKER results can be the result of additional hints sent to SNAP together with post processing to add UTR and additional exons that have support form transcript evidence. MAKER results will also have support from either protein or EST/mRNA evidence. SNAP match is simply the raw ab initio call made by SNAP (no hints, no post processing, and may or may not have evidence supporting the structure). They are there just for reference purposes. so you know what SNAP will produce outside of MAKER given the underlying HMM.

—Carson



On May 11, 2017, at 12:29 PM, Marcus Naymik <[hidden email]> wrote:

In the final GFF annotations what is the difference between a 'gene' from maker and a 'match' from snap?

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Re: Maker gene vs snap match in final GFF's

Ence,daniel
In reply to this post by Marcus Naymik
The two might have identical coordinates in some cases, but they are different kinds of features. The “match” is a product of an abinitio gene prediction algorithm, while the “gene” is is supported by evidence and passed through the maker polishing and filtering steps. 


On May 11, 2017, at 2:29 PM, Marcus Naymik <[hidden email]> wrote:

In the final GFF annotations what is the difference between a 'gene' from maker and a 'match' from snap?

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