Can Sorf Finder Suitable To Predict Sorfs For Prokaryotes?

Question

[Alyse]

Hi all,

From my understanding, all the training data sets for the sORF Finder program are from eukaryotes. So is sORF Finder suitable to use to predict sORFs for prokaryotes?

Thanks in advance. :)

Answer 1

[Torst]

sORF should work for prokaryotes, but you will have to install it locally and train it on prokaryotic example data. The website and paper focus on its use for large model eukaryotic sequences, but its parameters are changeable. For example, you will need to change the P(CDS) to be 0.9 as bacteria are coding dense, and I'm sure there are more things to tweak to get it working.