 
Dear list,
Anyone a pointer / piece of code on how to find genes that are closest
to a specific chromosomal location?
 
I am using Biostrings and associated mouse genome package to find and
localize specific sequences (putative TFBS). This works fine (thanks
Herve for the clear vignette). I have now an output (list) like this:
 
seqname start  end  strand patternID
chr1 7196884  7196895  +  GH_TEST
chr1 15433465 15433476 +  GH_TEST
chr1 78251474 78251485 +  GH_TEST
chr1 82635484 82635495 +  GH_TEST
chr1 22603411 22603422 -  GH_TEST
chr1 34167820 34167831 -  GH_TEST
chr1 47227452 47227463 -  GH_TEST
 
Next I would like to know which gene is closest to the each entry, and
what the distance is. 
For example, info like the first entry is situated 1234 bp upstream of
the TSS of gene ENSMUSG000xx, and entry 2 is located 3456 bp downstream
of the TSS of gene ENSMUSG00yy. Etc.
 
I am thinking of using BiomaRt for this, but I don't know how to do
this. 
 
Note: In the archive I did find a related thread but the functions given
unfortunately do not give the info I am after.
http://article.gmane.org/gmane.science.biology.informatics.conductor/509
7
 
Any suggestions are appreciated,
Guido
 
 

------------------------------------------------ 
Guido Hooiveld, PhD 
Nutrition, Metabolism & Genomics Group 
Division of Human Nutrition 
Wageningen University 
Biotechnion, Bomenweg 2 
NL-6703 HD Wageningen 
the Netherlands 
tel: (+)31 317 485788 
fax: (+)31 317 483342 
internet:   http://nutrigene.4t.com <http://nutrigene.4t.com/>  
email:      guido.hooiveld@wur.nl 



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