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Can I improve pathway calculation by adding Tier3 relatives?

asked 2016-08-25 08:22:34 -0600

anonymous user

Anonymous

When I use Pathway Tools to make a new database for a new organism, does it make sense to load Tier3 databases of closely related organisms into Pathway Tools to get more pathways? I mean, the Tier3 databases are calculated from what is already in Pathway Tools so it might not make sense, but they provide combinations of enzymes as occurred in related species so does that help Pathway Tools calculate more pathways?

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answered 2016-09-01 13:04:54 -0600

ptools-admin gravatar image

No, the Pathway prediction is only affected by the "reference" PGDB and the genome annotation itself. Besides the default reference PGDB of MetaCyc, it does not take into consideration other PGDBs that is accessible from Pathway Tools. Please refer to Chapter 7 of the UserGuide under the Help menu for details on how Pathologic works. There's also a paper that describes how the Pathway Prediction works: http://www.ncbi.nlm.nih.gov/pmc/artic...

The main way to improve Pathway Prediction is to improve the underlying genome annotation.

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Asked: 2016-08-25 08:22:34 -0600

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Last updated: Sep 01 '16