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

E Dimmer edimmer at ebi.ac.uk
Fri Oct 5 10:04:45 PDT 2007


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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