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Go Tree Trimming

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?

gene-ontology trimming
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updated by Florida • Florida • written by ewre ewre

1 answer

Hi ewre,

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

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updated by Ram Ram • written by Ben Sutherland • Ben Sutherland

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

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written by wilfried.souleyreau • wilfried.souleyreau

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