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Promoter prediction

| posted 13 Jul, 2020 21:09

One of my students is scanning for promoter sequences in our finished genomes. I was going to ask her to just focus on the gaps with more than 50bp but she tried the prediction tool in DNAMaster and the entire genome was analyzed in a few seconds (even though the manual mentions that this should not be the case because it is such a computationally intensive task). My question is with regards to how to interpret the scores. I am still asking her to zero in those 50bp gaps, and to not even look at anything with an overall score lower than 0.6, but this cutoff is a bit random. Is there a "this is definitely not a promoter cutoff"? Thank you!
| posted 13 Jul, 2020 21:14
Nope. No cutoff score per se, but bigger is better. I think I only look at top hits or areas of interest. But your approach is the one that sounds reasonable. It has to make sense.
| posted 13 Jul, 2020 21:19
Sounds good. Thank you!
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