[Bioperl-l] help on getting annotations
sdavis2 at mail.nih.gov
Wed Mar 16 06:38:34 EST 2005
A bit of an off-topic reply coming!
I just noticed that you are also posting to the BioConductor list about
some microarray-related issues. The BioConductor project has a package
called AnnBuilder that will build a HUGE annotation package for you
based on your genbank accession numbers. Then, you can have your
annotation AND microarray data available via R without having to read
various text files, etc. There are also R functions to perform all the
usual statistical analyses (enriched ontology categories, KEGG
pathways, etc.). If you are using R/Bioconductor to do your analyses,
you should really look at AnnBuilder and annotate packages (and related
On Mar 16, 2005, at 1:49 AM, zhihua li wrote:
> Hi netter!
> I have a series of GenBank Accession Numbers(GB78091, GB90876,...) and
> wanna get as much information as possible about each items. I want to
> know their UniGene ID so that I can tell if there are redundancies
> among them; I want to get their gene descriptions or GO annotations so
> as to group them into functional groups; I want to know their KEGG
> pathway IDs so that I can tell which of them are in the same
> biological pathway, etc.....
> Of course I could submit the seris of accession numbers to each
> different database (GenBank, GO, KEGG...) and get their annotations
> respectively. But as the seris contains a large number of items, I
> think it's better to write a perl script (or use an existing bioperl
> function) to have it done automatically.
> Could anyone give me a hint about how i can write the script or use
> the corresponding bioperl function? I'm new to both perl and bioperl.
> Thanks a lot!
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