MEME SUITE: tools for motif discovery and searching

Abstract

The MEME Suite web server provides a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains. The popular MEME motif discovery algorithm is now complemented by the GLAM2 algorithm which allows discovery of motifs containing gaps. Three sequence scanning algorithms--MAST, FIMO and GLAM2SCAN--allow scanning numerous DNA and protein sequence databases for motifs discovered by MEME and GLAM2. Transcription factor motifs (including those discovered using MEME) can be compared with motifs in many popular motif databases using the motif database scanning algorithm TOMTOM. Transcription factor motifs can be further analyzed for putative function by association with Gene Ontology (GO) terms using the motif-GO term association tool GOMO. MEME output now contains sequence LOGOS for each discovered motif, as well as buttons to allow motifs to be conveniently submitted to the sequence and motif database scanning algorithms (MAST, FIMO and TOMTOM), or to GOMO, for further analysis. GLAM2 output similarly contains buttons for further analysis using GLAM2SCAN and for rerunning GLAM2 with different parameters. All of the motif-based tools are now implemented as web services via Opal. Source code, binaries and a web server are freely available for noncommercial use at http://meme.nbcr.net.

Figure 1.

Overview of the MEME Suite tools.

Figure 2.

A sample GLAM2 gapped motif.

Figure 3.

Tomtom output. The figure shows the Tomtom output from searching a single DNA motif against a collection of yeast transcription factor binding site motifs identified via ChIP-seq (9). Tomtom shows that the query motif closely resembles the binding motif for transcription factor RGT1.

Figure 4.

FIMO output.

Figure 5.

GLAM2SCAN output. The figure shows the result of searching with a GLAM motif against 18 E. coli DNA sequences containing the Cyclic AMP receptor protein (CRP) binding site. Only the top 10 matches are shown.

Figure 6.

MAST output. The figure shows the result of searching with three MEME motifs against 18 E. coli DNA sequences containing the CRP binding site. The MAST output contains three representations of the results, excerpts of which are shown in the three figure panels. The E-value score of the overall match of the motif(s) in the input is shown in the first results section (Panel A). The second section (Panel B) displays the relative locations of significant matches of the motifs in the sequences. The third results sections gives a detailed picture of the motif matches, showing the exact location and p-value score of each motif match aligned above the target sequence.

Figure 7.

MEME Suite deployed with Opal (A) Opal offers versatile user access options. (B) Opal dashboard provides job history data.