[Bioperl-l] Need help for a GO request
skirov at utk.edu
Thu Oct 6 12:35:17 EDT 2005
There is bunch of ways to do that, including existing tools.
See genereg.ornl.gov/webgestalt and genereg.ornl.gov/gotm for example
(I believe it is doing precisely what you need).
You may need to convert your ids to entrezgene id:
go to genereg.ornl.gov/gkdb/->Gateway->ID conversion
You may also install locally the GO database from www.godatabase.org
(which is mysql).
ctemp2 at free.fr wrote:
>I have a list of genes (accession numbers) and I would like to find the
>associated informations in Gene Ontology (I work with those datas, find
>biological process, common node between 2 genes...).
>I am a newbie with Bioperl and I would like to know :
>- if there would be a module to send a request to the NCBI to obtain the GO
>informations for those genes
>- or if there would be a module to send the GO id to the GO site (I tried to use
>Bio::Ontology::SimpleGOEngine but the example doesn't work, I get an error with
>the 'parse' method which is not found by Perl in the module).
>Thanks if you can help me.
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>Bioperl-l at portal.open-bio.org
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