 
Dear list,
I am a novice in genome builds and have therefore some basic questions.
 
My ultimate goal is to identify the exact locations in the mouse genome
of several 'fixed' sequences, e.g. how many times is this specific
sequence "aaggggaaaaggtca", a putative transcription factor binding
site, present in the mouse genome, and more importantly, which genes are
closest to a match. After searching the archive I came to the conclusion
that the libraries Biostrings + BSGenome likely can do what I am after. 
http://thread.gmane.org/gmane.science.biology.informatics.conductor/1747
1
 
I understand the mouse genome in BSgenome.Mmusculus.UCSC.mm9 is build
based on data made available by the UCSC. I also noticed that the UCSC
MM9 assembly is also known as NCBI Build 37. However, my co-worker
always uses ENSEMBL to find info on genes...., but apparently ENSEMBL
also uses the same assembly (i.e. NCBI m37 mouse). Therefore:
- Am i correct; in other words, USCS and ENSEMBL use the same, identical
genome assambly? 
- Thus only the annotation of the genome differs between UCSC and
ENSEMBL?
- As a result, I can use the Bs.genome.xxx.mm9 to identify the locations
at the genome of a specific sequence, which I then can annotate using
ENSEMBL to identify the gene(s) that are closest to a match? And what
would be the best way of doing this? BiomaRt?
 
Thanks,
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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