Prokaryotic protein binding motifs databases

Question

[Andrew Sonin]

Hello.

I'm researching the promoters of bacterial and archean operons, and I would like to ask what data bases of DNA-binding motifs of prokaryotic regulatory proteins exist today?

Thank you in advance for any information.

Answer 1

[manuel.belmadani]

The MEME suite provides some prokaryotic databases of different sources: http://meme-suite.org/db/motifs

You can download them here: http://meme-suite.org/doc/download.html?man_type=web

You can either follow the description back to the source database, or use those since they're in MEME format, meaning they're readily usable with other tools in the MEME suite. For example, TOMTOM can take a predicted motif (IUPAC nucleotide, or a PSWM) and will align it to the entire motif set from the specified MEME format database(s), giving you p-value/E-values based on how strongly/distinctively your motif matches existing entries in the database(s).