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[gofriends] GO tool recommendations needed for demo to ~80 biologists new to GO.

John Matese jcmatese at genomics.princeton.edu
Fri Oct 5 11:25:47 PDT 2007


Hi Emily,

I believe our local implementation of GO-Termfinder fulfills most of  
your requirements:
http://go.princeton.edu/cgi-bin/GOTermFinder

Cheers,
John Matese


On Oct 5, 2007, at 1:04 PM, E Dimmer wrote:

> Hi,
>
> 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
>
> **
>
> O00548
> O14672
> P05067
> P25963
> P46531
> P49768
> P49810
> P50553
> P78504
> P78536
> Q04721
> Q06330
> Q0VG99
> Q12860
> Q12948
> Q16873
> Q4KMR2
> Q59ED8
> Q5SPL1
> Q5SSY7
> Q5STG5
> Q5SXM3
> Q5VTD0
> Q86UW9
> Q86Y01
> Q86YT6
> Q8IZL2
> Q8N9I9
> Q8NBS4
> Q8NFT8
> Q8WW43
> Q92542
> Q92585
> Q96AX9
> Q96BI3
> Q96JK9
> Q96T58
> Q99466
> Q99958
> Q9BRJ9
> Q9BYE0
> Q9H3D4
> Q9H488
> Q9HD90
> Q9NQ87
> Q9NR61
> Q9NYJ7
> Q9NZ42
> Q9UBP5
> Q9UBV2
> Q9UM47
> Q9UQ52
> Q9Y219
> Q9Y2E6
> Q9Y5J3
>
> -- 
> ************************************
>    Emily Dimmer
>    GOA Coordinator
>    EMBL-EBI
>    Wellcome Trust Genome Campus
>    Hinxton
>    Cambridge CB10 1SD, U.K.
>    Tel:     +44 1223 494654
>    Fax:    +44 1223 494468
>    email:  edimmer at ebi.ac.uk
> ************************************
>
>
> --
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