Question: Go Tree Trimming
0
gravatar for ewre
5.8 years ago by
ewre220
United States
ewre220 wrote:

HI,

GO is a database with a hierarchy structure. the upper level terms include the lower ones. I want to trim this tree at certain level to remove the redundancy. any tools to do this trimming process?

trimming gene-ontology • 2.1k views
ADD COMMENTlink modified 5.4 years ago by Ben Sutherland10 • written 5.8 years ago by ewre220
1
gravatar for Ben Sutherland
5.4 years ago by
Canada
Ben Sutherland10 wrote:

Hi hanguangchun,

If you want to remove redundancy between enriched terms in your output you could try the tool GO Trimming outlined in "GO Trimming: Systematically reducing redundancy in large Gene Ontology datasets" http://www.biomedcentral.com/1756-0500/4/267

with software provided here (also linked in the article): http://lucy.ceh.uvic.ca/go_trimming/cbr_go_trimming.py

ADD COMMENTlink written 5.4 years ago by Ben Sutherland10

Hi,

I would like to remove redundancy between enriched terms, but GO Trimming it's no longer working, the analysis starts and never ends. It might be because the database is too old ? Do you have a more recent database for Go Trimming ?

Thanks a lot, Regards, WS

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by wilfried.souleyreau0
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