[Bioperl-l] Database Retrieval

Cui, Wenwu (NIH/NLM/NCBI) [C] cuiw at ncbi.nlm.nih.gov
Mon Aug 7 11:25:48 EDT 2006

Hello, Rick:

Novartis does provide a flat text file for these data. You can simply
load it to either R or MySQL. If you want, I can share my scripts with


-----Original Message-----
From: Davis, Sean (NIH/NCI) [E] 
Sent: Monday, August 07, 2006 10:41 AM
To: Rick Scavetta; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Database Retrieval

On 8/7/06 9:58 AM, "Rick Scavetta" <RScavett at uni-koeln.de> wrote:

> Hello Programmers,
> I have a list of mouse GeneIDs for which I have extracted the RefSeqs
> With these accession numbers I want to know what are the three closest
> upstream and downstream genes (and orientation, if possible) to my
gene of
> interest. Is these some way of finding this out? Any suggestions?

I would look at using the UCSC genome browser data.  You can download
refGene table, order it by chromosome and start, then do whatever
manipulation you like.  Your problem can probably be solved with perl,
if you have experience using R (the statistics software), using it may
more straightforward.  You could also potentially do this using SQL
of the UCSC MySQL database.

Is there a reason to use "number of genes"?  If you can simply restrict
to a
number of base pairs, the problem can (probably) be solved using only
UCSC table browser.

> Also, I would also like to know something about the expression of a
> particular gene of interest. e.g. ba querying the Novartis Gene Atlas
> (http://symatlas.gnf.org/SymAtlas/). Is there a module for handling
> submissions and retrieving results of this sort?

No, but, again, UCSC hosts these data and they have nice query tools, a
publicly-accessible MySQL database containing the information, and
downloadable tables for the data.

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