Finding promoters, genes

[Bioinformatic1]

Hi, does anyone know where I can find a annotated database which specifically gives the genes and its promoters? I am new to bioinformatics and I need to analyse the promoters but I cant seem to find the right sources. Any suggestions will be much appreciated.

[GenoMax]

Here is a small set of tools for promoter analyses: http://molbiol-tools.ca/Promoters.htm

If you are only looking for databases then google is your friend. Here are a couple of examples: http://epd.vital-it.ch/ http://rulai.cshl.edu/CSHLmpd2/

[dariober]

Hi, does anyone know where I can find a annotated database which specifically gives the genes and its promoters? I am new to bioinformatics and I need to analyse the promoters but I cant seem to find the right sources. Any suggestions will be much appreciated.

Hi,

I don't think there is a clear understanding yet of what an eukariotic promoter exactly looks like and where it starts and finishes. Have a look at wikipedia http://en.wikipedia.org/wiki/Promoter_%28genetics%29 for a start.

Often genome-wide studies consider the "promoter" of a gene the region around the transcription start site. Typical regions are 100 or 1000 bp downstream and upstream the start site or 100bp downstream and 1000 bp upstream (since the promoter is expected to be upstream) or something on these lines. As I said, there is no clear cut definition as far as I know.

So your question could be reformulated as "Where do I get the position of the transcription start sites?" and the answer is UCSC genome browser or ensembl, if your species is there.

Hope this helps
Dario