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GO and C.elegans yk clones

Eleanor Whitfield eleanor at ebi.ac.uk
Wed Oct 1 03:12:13 PDT 2003


Hi,

just a little background if you wish to read on ...

>     gene_association.wb is the standard GO gene associations
> flatfile (in tab-delimited format) for C. elegans.

GO associations from the WormBase team are:
InterPro2GO IEA mappings.  These are drived from the InterPro crossreferences in
the related Swiss-Prot and TrEMBL entries.
Manual annotations done by the Caltech group within the project.

> yk2orf.WS110 is
> the newly-introduced WormBase flatfile showing linkages between yk
> clones and genes.

The yk clones are Yuji Kohara EST clones (5', 3' and full length).  The file
yk2orf.WS110 makes the correspondence between the yk clone names and the cosmid
based gene names eg AH6.1 etc.  As a consequence there may be a many to one match
from EST to cosmid name.
WS110 is the current WormBase release date, releases are approximately every
fortnight.

The GO annotations for each gene are found on the 'Gene summary' page only as a
row in the table presentation of the data.  The only file of all annotations
together are found at the GO site, not in WormBase.

thanks
Eleanor Whtifield
(Swiss-Prot annotator of C.elegans genome project)


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