Any new recommended protocol for gene prediction, if you have isoseq data??

Question

[karthic]

Dear all,

I would like to get some suggestions/recommendations regarding gene prediction for a repeat rich eukaryote genome. We have pacbio isoseq data for some tissues and also illumina based transcriptomes.

Does the availability of isoseq data mandates any new method or I should just follow the established methods.

Thanks, Karthic K

[karthic]

should I cluster the protein sequences of related organisms I have downloaded from NCBI protein??