EMBOSS predicting proteins
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2.8 years ago
MK2000 ▴ 30

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 • 613 views
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2.8 years ago
h.mon 33k

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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