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EMBOSS predicting proteins

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!

emboss protein prediction metagenomics
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updated by h.mon h.mon • written by MK2000 • MK2000

1 answer

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/

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written by h.mon h.mon

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