I am currently doing eukaryotic genome annotation. I have done the structural annotation and Protein functional annotation. I did not follow the order of NCBI, which is determine the gene model with cmsearch result. NCBI annotation pipeline After reading the manuals, I am confused with the information I got:

1. Should I use cmscan + Rfam/ or combination of tools listed in Infernal manual

   tRNAscan-SE for tRNAs

   RNAMMER for rRNA

   snoscan for snoRNAs

   SRPscan for SRP RNA

2. Anything I should consider more carefully with the command provided? (modify the threshold or anything else)

   nohup cmscan --cpu 96 -Z 2276.006224 --cut_ga --rfam --nohmmonly --tblout beltfish_ncRNA.tblout --fmt 2 --clanin ~/output/Rfam.clanin ~/output/Rfam.cm ../beltfish_genome_1.fasta > beltfish_ncRNA.cmscan 2> beltfish_ncRNA_error.log &

Thanks~