Dear Friends Hi (*'m not native in English!*)

I want to search for orthologs locally using EggNOG in my **fish** transcriptome samples.

First I have download [fiNOG][1] which is specially for fishes from [EggNOG][2],

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][3] ?* )?

Thank you


  [1]: http://eggnogdb.embl.de/download/eggnog_4.5/data/fiNOG/
  [2]: http://eggnogdb.embl.de/#/app/seqscan
  [3]: https://transdecoder.github.io/
There is now a better resource for functional annotation using eggNOG orthology. Check these links:

*Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper*

 - http://eggnog-mapper.embl.de (online tool)

 - http://biorxiv.org/content/early/2016/09/22/076331 (method description and benchmark) 

 - https://github.com/jhcepas/eggnog-mapper  (eggnog-mapper tool. Use the option --translate if using nucleotide seqs)