Regulatory region searching.. (bioinformatics)

[Jikx]

I've been given the neucleotide gene sequence for a protein, and been told to find out the regions where the gene is regulated. Unfortunately, the website database where they told me to go is dead!

I've tried BLAST (http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi)ing the sequence, but all I get is the protein it creates, with a whole mish-mash of tiny unrelated proteins. It doesn't tell me the sequence which could be regulating it...

Can anyone help here? Basically looking for a website that allows me to search within sequences to find any homologies with known regulatory sequences.

Thanks a bunch!

[iansmith]

You may want to use this
Promoter Prediction (http://www.fruitfly.org/seq_tools/promoter.html). this program will give you an idea where the promotor is and you look at the region by eyes to see an regulatory elements

If you browse Expasy Molecular biology server (http://au.expasy.org/) you migth find some other program that can be used

[iansmith]

At this web site http://www.gene-regulation.com/pub/programs.html, there is also a list of program that you may use for promoter prediction and DNA binding

[Monique]

I use two sites, one is DBTSS (database for transcription start sites) it will be the first one to show up in Google. You can look up the gene you are interested in, you can then make an excision of the promotor sequence around the tss.

Another very good website is www.genomatix.de, you'll have to register and there are a limited amount of searches you can do per month as an academic person, there are dozens of things you can do in there, among them gene2promotor: retrieving and analyzing promotors.

Genomatix.de should be the perfect website for you, if you want to find out transcription factor binding sites. If you are looking for more general binding sites like a TATA box, a cozack consensus sequence, it might be too complex.

[Jikx]

thanks all ! Life savers :)