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PensacolaC28 Start calling question

| posted 09 Feb, 2024 20:41
Hi all,
We have some questions on 2 gene starts in PensacolaC28

The first is gene 1 (stop 1611). Glimmer calls the start at 37, and GM at 1. I thought conventionally gene 1 started at nucleotide 1, but RBS favors start at 37. We are wondering if RBS only favors start 2 because it can't accurately calculate where the circular genome is cut?

Next we have Gene 14 (12501 stop). We believe 16 is not a gene, and plan to delete it. On gene 14 glimmer calls the second start. but calling the first start at 12172 eliminates a 100bp gap, however the glimmer start has a great score. It also does not include any additional GM coding potential. We're pretty torn on this call

Any advice is appreciated, thanks!
| posted 09 Feb, 2024 21:52
Hi Emily,
Both are good questions.

For the first gene, the coding potential on the GeneMark output is rather robust upstream of 37. How would you evaluate the ability of that gene to start if you are evaluating a start at base 1. What do you want to see upstream of a start to evaluate the start? How would you do that in this case? Why do you say that RBS only favors the second start?

For the second gene, how is that gene going to be made? What favors the best production of that gene?

Keep thinking!
What did you professor have to say?
Edited 09 Feb, 2024 21:54
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