Pathway Tools Question & Answer forum for SRI's Pathway Tools

Can I improve pathway calculation by adding Tier3 relatives?

asked 2016-08-25 08:22:34 -0500

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?

edit retag flag offensive close merge delete

add a comment

1 Answer

Sort by » oldest newest most voted

answered 2016-09-01 13:04:54 -0500

ptools-admin
468 ●10 ●14 ●15

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.

edit flag offensive delete link

add a comment

Your Answer

Please start posting anonymously - your entry will be published after you log in or create a new account.

Add Answer

Question Tools

1 follower

Stats

Asked: 2016-08-25 08:22:34 -0500

Seen: 567 times

Last updated: Sep 01 '16