Sequence -> putative DNA binding proteins Database

Question

[QVINTVS_FABIVS_MAXIMVS]

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!

[Denise CS]

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.

[natasha.sernova]

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