hi yanqin,
you need to make your own, unless someone who's made one is willing to
make it
available. i sent the same email around a few months ago on this list
with no
success.
if you feel up to it, check the annbuilder package, i was told that
was a good
place to start for making one yourself.
i did put this on my list of useful things to do though. that and one
for the
coli asv2 chip as i work with both, so if i get around to it, i'll let
you
know.
hth,
caroline
Quoting Yanqin Yang <yanqin_yang at="" yahoo.com="">:
> Hi,
>
> Does anyone know where I could find the annotation package for
> Affymetrix E_coil_2 chip? There are only ecoil2cdf and ecoil2probe
> packages available in the Annotation packages list.
>
> Thanks!
>
> Yanqin
>
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--
Caroline Lemerle
PhD student, lab of Luis Serrano
Structural Biology and Biocomputing Dept
tel 00-49-6221-387-8335
--
Hi, Caroline and Yanqin,
It is not easy to generate annotation packages for E. coli by using
AnnBuilder,
more specifically the ABPkgBuilder function. The set of source
databases we used
don't provide annotations for GO, UniGene, genome map location,
PROSITE and PFAM
for E. coli. For the rest of the annotations: gene name, symbol,
PubMed and
Refseq mappings are from Entrez Gene, pathway and enzyme information
are from
KEGG. All annotations are based on Entrez Gene ID.
If there is a better Gene Identifier in the E. coli community (other
than Entrez
Gene ID) or if you have a better source than Entrez Gene or KEGG, it
will make
more sense to create a seperate builder for E. coli annotations than
to
manipulate ABPkgBuilder.
If you think Entrez Gene and KEGG are good sources for E. coli
annotation, then
we can try to "hack" ABPkgBuilder. If you could provide the sources
for the
missing annotations, I can help you to "hack" ABPkgBuilder or maybe
build the
package for you.
thanks
nianhua
Nianhua Li
Computational Biology, PHS, FHCRC
