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

Stefan Goetz sgoetz at cipf.es
Wed Oct 10 03:37:34 PDT 2007


Hi Emily.
Blast2GO would be a possible option for a GO tool demo as it full fills 
most of the given criteria and is course/workshop proved. We invite you 
to test B2G by yourself since it is really easy to start-up and use (if 
you have Java installed). Just import your list of genes with "import 
accession list" as ".acc" file and use nearly all the chart and graph 
options B2G offers. If you need any further support, information or 
material please do not hesitate in contacting us.
Best regards,
Stefan Goetz



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
>


-- 

--------------------------------------------
Stefan Gštz
Bioinformatics Department
Centro de Investigaci—n Pr’ncipe Felipe (CIPF)
C/E.P. Avda. Autopista del Saler, 16-3 (junto Oceanogr‡fico)
46013 Valencia, Spain
Tel: +34 963289680 Ext. 1011
Fax: +34 963289574
E-Mail: sgoetz at cipf.es
http://bioinfo.cipf.es
--------------------------------------------

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