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I am trying to build a machine learning training set for bacterial protein sequences that form biofilm, and that cannot. I collected the positive sequences from the GO ontology website but for negative sequences I am not sure which sequences to incorporate into my training set.

Can anyone point me to resources for proteins sequences that are known to be not capable of forming biofilms?

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Intracellular proteins cannot form biofilms. Additionally, many (but not all) extracellular proteins contain an N-terminal cleavable signal sequence.


Lory (1992) Determinants of extracellular protein secretion in Gram-negative bacteria. J Bacteriol 174: 3423-3428. https://www.ncbi.nlm.nih.gov/pubmed/1592799

Schneewind & Missiakas (2012) Protein secretion and surface display in Gram-positive bacteria. Philos Trans R Soc Lond B Biol Sci 367:1123-1139. https://www.ncbi.nlm.nih.gov/pubmed/22411983

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