One of the most frequently-asked questions we get when we are out doing workshops is: how do I find motifs in promoters, and what can I do with them to find more information? Just last Friday we were asked this again at the workshops we did at USC. So for this week’s tip of the week I’m going to show one of the tools I recommend for that purpose–Melina II. (I also recommended the MEME Suite and VISTA‘s rVISTA features as well, but for this tip I’ll focus on Melina.)
Melina II is not a new tool, it’s been around for a while. But it’s been one of my favorites because of the way it combines several tools that I would otherwise have to access separately. And I like the graphical representation that it delivers for the motifs that are discovered.
As they say on their homepage, it’s a straightforward 3-step process: put in some sequences, choose motif finders and set parameters, and then run to see your results. And it is just that easy. You can go in and tweak all of the motif finder parameters if you like, but a default setting search will quickly get you started finding motifs from an input set of sequences.
You’ll have a graphical display of the motif location in the sequence panel at the top, but you can click on any of the colored discovered motifs to display the alignments, the sequence logo, or the weight matrix at the bottom. And from there you could also do a couple of searches of other resources as well to locate additional promoters that may carry your motif.
It’s such a quick and slick way to look for motifs it has long been one of my first choices for this kind of analysis. You can access each of the individual motif finder tools at their home sites as well, and there may be more features over there. But to get started this is a very nice choice.
Note: A couple of weeks ago the Melina II tool was down, because of server issues. We talked with the team and although it’s up and running on a backup server, some of the settings aren’t quite right yet. But I still wanted to discuss it because of answering that question from the workshop. So you can try it out, but check back at a later date for the full server with the correct settings.
Find Melina II here: http://melina2.hgc.jp/
Okumura, T., Makiguchi, H., Makita, Y., Yamashita, R., & Nakai, K. (2007). Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions Nucleic Acids Research, 35 (Web Server) DOI: 10.1093/nar/gkm362
(We have just updated our full tutorial version of the Melina II tool, which is available for individual purchase or by subscription here.)