Hi , I am using GeneMarkS (v 4.30) to generate the gene prediction models for a bacterial genome using:
gmsn.pl --prok --faa genome.fasta --verbose
This outputs three model files: GeneMark_hmm_heuristic.mod, GeneMark_hmm.mod and GeneMark_hmm_combined.mod
I would like to apply the GeneMark algorithm on a list of nucleotide sequences of interest (fasta) to identify the most likely translation start site in each one.
Any advice on the differences between the model files above, and which program from the GeneMark suite to use for this purpose, will be much appreciated. I suspect I can use one of the above models with GeneMark.hmm, but cant find it in the documentation exactly. Also, what is the difference between GeneMark.hmm and GeneMark?
Thanks a lot