In this week’s tip I’m going to introduce you to a suite of motif discovery tools, and show you (briefly) how to use one of the tools. The MEME suite is a comprehensive collection of tools for analysis of both protein and DNA motifs. As described on the MEME Suite homepage, or in the citation that I reference below, this set of tools allows one to use as much or as little of the suite as meets their research needs. A user can initially find motifs with either the MEME or GLAM2 algorithm. The original motif discovery algorithm created by the developers, MEME, finds ungapped motifs within DNA or protein sequences. GLAM2 specializes in the discovery of gapped motifs. The motifs found with either of these tools can then flow directly into the downstream tools of the suite for further analysis.
There are three different tools that can be used to search a sequence database for motifs. MAST and FIMO use different algorithms but both use MEME output or ungapped motifs to search sequence databases. GLAM2SCAN uses the gapped motif output from GLAM2 to search sequence databases. There is also the tool, TOMTOM, which allows you to compare your motif to a database of motifs to find any matches. The GOMO tool finds gene ontology terms that are associated with genes regulated by a motif, to add functional information about a motif.
All of these tools together create a comprehensive, unified site for the discovery and analysis of sequence motifs. Researchers can begin with unaligned sequences and use the MEME suite of tools to find motifs and obtain: aligned motifs, annotated sequences, or annotated motifs. This suite has been thoughtfully designed to allow you to find motifs with MEME and GLAM2 and then easily – with just a click of a button – perform further analysis with MAST, FIMO, GLAM2SCAN, TOMTOM and GOMO.
I cannot begin to show the utility of the whole suite in this short tip, but if you are doing motif discovery, alignment or analysis I’d suggest that you check out these tools for yourself. If you are interested in further details on MEME, you can check out our MEME Suite tutorials, check out the documentation on the site (it is clear & pretty comprehensive), or check out their paper in the database issue of the journal Nucleic Acids Research. The paper is well written & provides a nice overview of how data can flow through the suite, as well as some details on each specific tool in the suite.
Bailey, T., Boden, M., Buske, F., Frith, M., Grant, C., Clementi, L., Ren, J., Li, W., & Noble, W. (2009). MEME SUITE: tools for motif discovery and searching Nucleic Acids Research, 37 (Web Server) DOI: 10.1093/nar/gkp335