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Does GeneMark identify all potential start sites?

Link to this post \| posted 21 Jun, 2018 20:18
MSMC	In looking at the coding potential for potential start sites, I was under the assumption that GeneMark identified all potential start sites (not the coding potential, but the ATG, TTG and GTG start sites). For this gene, the start with the longer ORF at 41175, which is annotated more often, does not show up on the GeneMark output. Is there a reason GeneMark would omit a potential start site? Maybe it does this and I haven't noticed in the past. Edited 21 Jun, 2018 20:19 46Kb 39Kb

Link to this post | posted 21 Jun, 2018 20:18

MSMC

In looking at the coding potential for potential start sites, I was under the assumption that GeneMark identified all potential start sites (not the coding potential, but the ATG, TTG and GTG start sites). For this gene, the start with the longer ORF at 41175, which is annotated more often, does not show up on the GeneMark output.

Is there a reason GeneMark would omit a potential start site? Maybe it does this and I haven't noticed in the past.

Edited 21 Jun, 2018 20:19

Link to this post \| posted 21 Jun, 2018 21:56
debbie	Evan, GeneMark does call all starts ATG, GTG, and TTG (you will find that GenMark can agree with Glimmer on a TTG start in DNA Master). However, GeneMrk's graphic output is only coded to represent ATG (longer upticks) and TTG (shorter upticks) starts. I think they ran out of money to update all of the graphic displays…..

Link to this post \| posted 22 Jun, 2018 11:08
MSMC	That makes sense, thanks Debbie!