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[gofriends] GO tool recommendations needed for demo to ~80 biologists new to GO.
jcmatese at genomics.princeton.edu
Fri Oct 5 11:25:47 PDT 2007
I believe our local implementation of GO-Termfinder fulfills most of
On Oct 5, 2007, at 1:04 PM, E Dimmer wrote:
> I'm looking for a tool to demonstrate during a couple of
> 'Introduction to GO' talks/tutorials and I would be extremely
> grateful if some tool developers/users could help me choose one.
> As the audience would be mainly composed of biologists looking at
> resources that work with UniProt data, I'm looking for an online
> tool that clusters UniProt protein accessions to display over-
> representation of GO terms. I need a simple, effective tool that:
> 1. is freely available
> 2. can accept human UniProt Accession numbers as input (e.g. Q9Y5Q8)
> 3. can temporarily cope with the load of ~ 40 people accessing the
> tool simultaneously (if the tool can alternatively be locally
> installed, thats fine too)
> 4. provides a simple interface and outputs a graphic showing
> showing clustering of proteins around a GO node (if the tool can do
> more that's fine, but for the limited time-span of the tutorials I
> need users to easily understand the main idea of the tool and have
> results returned quickly)
> 5. finds statistical significance using a multiple-testing correction
> 6. appreciates the GO DAG, GO evidence codes, and has removed 'NOT'
> annotations from any imported GO annotations.
> 7. provides full documentation and is fully supported
> 8. updates regularly with the GO gene association and OBO files
> (monthly would be ideal)
> If you have/use a tool which meets all these requirements, could
> you please let me know?
> At the bottom of this e-mail I have listed 55 human UniProt
> Accessions which all have an annotation to the GO term 'Notch
> signaling pathway' (GO:0007219) or one of its children, an example
> of one of the dataset I might supply for the demo.
> If I find more than one tool that meets the above requirements, I
> will at least advertise them all, even if I can not demo each of them.
> Thanks very much,
> Emily Dimmer
> GOA Coordinator
> Wellcome Trust Genome Campus
> Cambridge CB10 1SD, U.K.
> Tel: +44 1223 494654
> Fax: +44 1223 494468
> email: edimmer at ebi.ac.uk
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