[BioC] Help with promoter analysis

[Yuan Hao]

Hi Davy,

This is a bit off the topic of the list, but hope it could be of help  
some others.

My personal experience is biomart is based on Ensembl gene  
annotations, which won't be exactly the same if you adopt another  
annotation, like UCSC,  in terms of gene names, transcripts... Apart  
from the differences may exist in mitochondria genome included by  
these two databases, I believe the master majority of the genes are  
the same coordinated on the genome, so it should be ok to download the  
promoter sequences from either, and biomart is quite efficient on this.

In terms of motif searching, it's really depends on the programs/ 
tools, i.e. the algorithms, you pick up to use.

Cheers,
Yuan

P.S. Promoters from UCSC could be retrieved from its table browser.


On 27 Feb 2012, at 14:14, Davy wrote:

> Thanks Alex and Yuan,
> One last question though.
>
> Is biomart capable of downloading the promoter sequences of every  
> gene in
> the genome, and would searching all those sequences not be very  
> expensive
> in terms of memory?
>
> Cheers,
> Davy
>
> -- 
> David Kavanagh
> Nephrology Research, Centre of Public Health, Queen's University  
> Belfast, A
> floor, Tower Block,
> City Hospital, Lisburn Road, BT9 7AB, Belfast, United Kingdom
>
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