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Considering the Path-A based metabolic pathway prediction (http://nar.oxfordjournals.org/content/34/suppl_2/W714.short). It uses machine learning for pathway prediction. Suppose that the input was a protein sequence of a query organism. I do not understand what these protein sequences are? Are these the enzymes for the reactions?

The basic algorithm has two inputs: a set of protein sequences from the query organism and a set of model pathways, one for each target pathway.

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Not necessarily, they can be enzymes, but they include a lot more (the whole proteome).

It takes a FASTA format file containing a set of query protein sequences from a single organism (a partial or complete proteome) and identifies those sequences that are likely to participate in any of its supported metabolic pathways

Path-A predicts the pathways supported by arbitrary sets of proteins, using validated prediction techniques based on sequence alignment and machine learning.

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  • $\begingroup$ The whole proteome as in the whole genetic sequence available? $\endgroup$ – girl101 May 23 '15 at 11:34
  • $\begingroup$ @Rishika No, the proteome. $\endgroup$ – MattDMo May 23 '15 at 18:22
  • $\begingroup$ so basically a proteome is the list of all the available proteins in an organism?? $\endgroup$ – girl101 May 26 '15 at 7:38

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