AME & RAMEN - Detect relative enrichment of motifs

As part of my PhD, I developed two additional tools, AME (Analysis of Motif Enrichment) and RAMEN (Regression Analysis of Motif ENrichment), which support various methods of detecting enrichment of motifs or transcription factor binding sites.

As the paper abstract states:

A major goal of molecular biology is determining the mechanisms that control the transcription of genes. Motif Enrichment Analysis (MEA) seeks to determine which DNA-binding transcription factors control the transcription of a set of genes by detecting enrichment of known binding motifs in the genes’ regulatory regions. Typically, the biologist specifies a set of genes believed to be co-regulated and a library of known DNA-binding models for transcription factors, and MEA determines which (if any) of the factors may be direct regulators of the genes.

This tool is part of the MEME Suite, and is available for free use online here:

• AME and RAMEN - MEME Suite

Since originally developing it back in 2010, it has continued to be improved and extended by the MEME Suite team. The original publication can be found here:

• Motif enrichment analysis: A unified framework and an evaluation on ChIP data.
  McLeay, R. C. and Bailey, T. L. (2010). BMC Bioinformatics, 11, 165.