Question: protein binding sites
0
gravatar for yueli7
10 months ago by
yueli7140
China
yueli7140 wrote:

Hello,

I have around 200 protein's fasta file. How can I find these proteins binding site with DNA?

For example:

The AP-1 binding site, also known as the AP-1 promoter site, is a DNA sequence to which AP-1 transcription factors are able to bind. The AP-1 binding site, in humans, has a nucleotide sequence of ATGAGTCAT.

Thanks in advance!

Best,

Yue

gene • 327 views
ADD COMMENTlink modified 10 months ago by urdupakistannetwork0 • written 10 months ago by yueli7140

Are there any databases that contain this information? How did you get the information on AP1, for instance?

ADD REPLYlink written 10 months ago by RamRS27k

Hello, RamRS,

Thank you for your reply!

It comes from Wikipedia.

AP-1 Binding Site From Wikipedia, the free encyclopedia Jump to navigationJump to search The AP-1 binding site, also known as the AP-1 promoter site, is a DNA sequence to which AP-1 transcription factors are able to bind.The AP-1 binding site, in humans, has a nucleotide sequence of ATGAGTCAT.

Thank you again!

Best,

Yue

ADD REPLYlink written 10 months ago by yueli7140

Wikipedia is not a good primary source of information. Can you find a database that has this entry? Unless there's a database (or journal articles open to full text crawling + NLP), collecting this data will need to be manual.

ADD REPLYlink written 10 months ago by RamRS27k

There are a lot of similar posts in 'Bioostars.org'.

See the right panel of your own question and choose what exactly you need:

Protein Dna Binding

Is There A Database Of Known Dna Binding Proteins?

For transcription factors, for example:

How To Obtain Encode Tfbs Using The Ucsc Genome Browser

Sequence -> putative DNA binding proteins Database

Transcription Factor Dna-Binding Sites

DNA-binding sites to proteins in bacteria

etc...

ADD REPLYlink modified 9 months ago • written 9 months ago by natasha.sernova3.7k
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