Question: Sequence -> putative DNA binding proteins Database
1
gravatar for QVINTVS_FABIVS_MAXIMVS
4.6 years ago by
USA SoCal
QVINTVS_FABIVS_MAXIMVS2.4k wrote:

I'm looking for a database where you input a DNA sequence and get putative DNA binding proteins (Transcription factors, nuclear receptors, anything other than histones really)

Does such a database exist?

Thanks!

ADD COMMENTlink modified 4.6 years ago by natasha.sernova3.8k • written 4.6 years ago by QVINTVS_FABIVS_MAXIMVS2.4k
1

Without knowing the species you are interested in, what I can comment on is that in Ensembl, we have annotated regions of the human and mouse genomes where TF binds to (TFBS), in addition to regions of open chromatin and histones modifications, that you are not interested in. These data come from ENCODE, Blueprint and Roadmap projects and are available pre and post-processing (the later gives rise to the Ensembl Regulatory Build) You could run a BLAST/BLAT for your sequence(s) using our web tool (providing your species is in Ensembl) and from the BLAST hits, go to the Ensembl browser (see this video for a demo) to check whether or not we've annotated the region as being a TFBS e.g. this CTCF binding site within the interval 17:64362495-64363617.

ADD REPLYlink written 4.6 years ago by Denise CS5.1k
1

This is a new server, I hope it may be helpful to you.

It studies the solved structures of protein-DNA-complexes.

http://npidb.belozersky.msu.ru/

https://nar.oxfordjournals.org/content/44/D1/D144.full

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by natasha.sernova3.8k
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