EMBOSS predicting proteins

Question

[MK2000]

I am trying to follow the data analysis of a paper, and they vaguely say "predicted protein sequences from metagenomic reads using EMBOSS". For anyone familiar with EMBOSS features, would you go with getorf command or transeq?

Thank you!

Answer 1

[h.mon]

If you are predicting proteins directly from the reads, getorf is the more appropriate tool, as it output all possible orfs (each as a separate sequence), while transeq will output just one translation - by default, the forward first frame.

You may want to look at OrfM: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5013905/