[Bioperl-l] help on getting annotations

[Sean Davis]

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 
GOStats).

Sean

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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