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I doing experimentation for peptide prediction using machine learning. I need some data for testing. My background is Computer Science.

Any advice how to find proteotypic and non-proteotypic peptides. I already got one dataset "Y.pestis". However, I'm looking for another dataset (for verification). For example, S.typhimurium or S.oneidensis, but any other peptides will be OK.

I tried PRIDE archive, but I couldn't figure out how to get two datasets; one for proteotypic and another for non-proteotypic

Any advice is appreciated!

Thanks!

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  • $\begingroup$ I suppose anyone answering this question would already know what a proteotypic peptide was. I don't find the definition totally clear from brief literature searching. From your question it would seem to mean a peptide that is unique for the proteome of one organism. Is that so? Do you know how the Y.Pestis dataset was prepared? I should imagine it was done computationally, in which case it would presumably be easy to apply to any other characterized bacterial genome. $\endgroup$
    – David
    Jun 30, 2016 at 12:31
  • $\begingroup$ Yes, peptide that is unique for the proteome of one organism e.x E.coli $\endgroup$
    – user836026
    Jun 30, 2016 at 12:36

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