Dear Friends Hi ('m not native in English!)
I want to search for orthologs locally using EggNOG in my fish transcriptome samples.
then built a HMMER database using hmmpress (i.e.
cat fiNOG_hmm/*.hmm > fishDB.hmmer), and run hmmpress fishDB.hmmer.
then I intend to run such script :
hmmscan --cpu 24 '/home/fiNOG_hmm/fishDB.hmmer' '/home/Transcriptome.fasta'
My question: Can I use my transcriptome assembly .fasta file directly in this script or I must convert (translate) it into protein in advance (which tool is better for this job? Transdecoder ? )?