[Genome] Finding nearest genes to a given genomic position

[Hiram Clawson]

Good Morning Christoph:

Please note this example of fetching nearby genes using the public
MySQL server:

http://genomewiki.ucsc.edu/index.php/Finding_nearby_genes

--Hiram

Christoph Bock wrote:
> Hello,
> 
> given a list of genome positions, can the UCSC Genome Browser or Galaxy
> retrieve me the nearest genes for each position in the list? 
> 
> More precisely, I have a custom track of genome positions in BED format
> (e.g. chr20	23917669	23917670), and I would like to obtain the
> RefSeq IDs of the closest gene both upstream and downstream, as well as
> their distance from the given position.
> 
> I found a previous posting asking a similar question
> (http://www.soe.ucsc.edu/pipermail/genome/2004-April/004533.html), but since
> this dates back three years already and pre-dates the current Galaxy, I was
> thinking that there may be a simple solution now. The "intersect" function
> unfortunately cannot solve this question, for obvious reasons.
> 
> Thank you and best regards,
>  Christoph
> 
> ___________________________________________________________
> 
>   Christoph Bock
>   Max-Planck-Institut für Informatik
>   Department of Computational Biology
>   Stuhlsatzenhausweg 85  /  66123 Saarbrücken  /  GERMANY
>   Office (Room 522): +49-681-9325-322
>   Fax: +49-681-9325-399
>   http://www.christoph-bock.de
> ___________________________________________________________