How to choose automatically the most representative (widely used) strain for bacteria species

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6.9 years ago

Juan Cordero ▴ 140

Hi,

I'd like to build a tree from the uniprot proteomes (see table in uniprot). However, for many bacterial species, there are plenty of strains I would like to exclude such that I only account for the most widely used or the most representative (in the case of E. coli, K12 strain for instance).

Does anybody know where I can get the most representative strain from the whole set of strain for a given species? 9853 proteomes is such a large number to do it manually...

bacteria choose reference strain proteomes • 1.4k views

ADD COMMENT • link 6.9 years ago by Juan Cordero ▴ 140

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Not sure if "widely used" has a comprehensive answer. You may have to pick and choose yourself. Are you planning to use a specific protein?

ADD REPLY • link 6.9 years ago by GenoMax 141k

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Sure, widely used might be misleading. What I mean is the most used strain as a model, such as K12 for E. coli. I need to use all proteomes in general, without focusing on any individual protein.

ADD REPLY • link 6.9 years ago by Juan Cordero ▴ 140

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