Do you recommend any tool that can predict surface proteins in selected bacteria strain e.g. Escherichia coli?
Many thanks for any suggestions,
Usually, these types of tools are specific to an organism if you are not looking for a general annotation tool, like Prokka, which would likely annotate surface protein genes.
For E. coli there is
SerotypeFinder: which requires assemblies
https://cge.cbs.dtu.dk/services/SerotypeFinder/ (web service)
(code behind webservice)
ABRicate which has two E. coli databases (EcOH and Ecoli VFdb) but requires assemblies: https://github.com/tseemann/abricate
seq_typing: which can take either reads or assemblies and predict E coli O and H antigens: https://github.com/B-UMMI/seq_typing
SRST2: same db's as Abricate, takes reads https://github.com/katholt/srst2#using-the-vfdb-virulence-factor-database-with-srst2
I'm sure there are more out there, but this is a good start.
Thanks! I will try that tools. Best, Agata
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