The bioBakery help forum

ARO id to antibiotics clusters

Hi,

May i know that how i can cluster the antibiotics families quantified from ShortBRED to larger antibiotics resistant group based on ARO id? like the heatmap in 2015-paper?

Those families were a result of the initial clustering step in ShortBRED. Specifically, proteins of interest are clustered based on high identity and coverage using CD-HIT and then multiply aligned with MUSCLE. A single member of the cluster is chosen as a representative for naming purposes.

Thanks franzosa.
Actually i encountered another problem when using shortbred_identify.py. it shows there are some invalid id in my sequence file. I need to use utils/AdjustFastaHeadersForShortBRED.py. But i can not find this utils. When i call python utils/AdjustFastaHeadersForShortBRED.py, it says no such file.

I installed ShortBRED using conda. And also can not find this package under python’s site-package folders.