Regulatory region searching (bioinformatics)

In summary, this website tells you about a protein and where the gene is regulated. However, the website is no longer up and running, so the person looking for this information is out of luck. There are other websites that can be used to find out about the promoter and the regulatory regions for the gene.
  • #1
Jikx
207
0
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 BLASTing 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!
 
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  • #2
You may want to use this
Promoter Prediction. 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 you migth find some other program that can be used
 
  • #3
  • #4
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.
 
  • #5
thanks all ! Life savers :)
 

1. What is a regulatory region?

A regulatory region is a section of DNA that controls the expression of nearby genes. It contains specific sequences that interact with regulatory proteins to turn genes on or off, allowing cells to respond to different stimuli and maintain proper gene expression.

2. How is regulatory region searching performed in bioinformatics?

In bioinformatics, regulatory region searching is typically performed using computational tools and algorithms. These tools analyze DNA sequences and identify potential regulatory regions based on known regulatory sequences and patterns.

3. What is the importance of regulatory region searching in bioinformatics?

Regulatory region searching is important because it helps us understand the complex mechanisms of gene regulation. It can also aid in identifying potential disease-causing mutations in regulatory regions and predicting the effects of these mutations on gene expression.

4. What types of regulatory regions can be identified through bioinformatics?

Bioinformatics can identify various types of regulatory regions, including promoter regions, enhancers, silencers, insulators, and transcription factor binding sites.

5. Can regulatory region searching be applied to non-human organisms?

Yes, regulatory region searching can be applied to any organism with a known genome sequence. It has been used to study gene regulation in a wide range of species, from bacteria to plants to humans.

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