GimmeMotifs for transcription factor motif analysis

What is GimmeMotifs?

GimmeMotifs is an analysis framework for transcription factor motif analysis written in Python. It contains command-line scripts to predict de novo motifs, scan for known motifs, identify differential motifs, calculate motif enrichment statistics, plot sequence logos and more. In addition, all this functionality is available from a Python API.

GimmeMotifs is free and open source research software. If you find it useful please cite our paper:

  • van Heeringen SJ and Veenstra GJC, GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments, Bioinformatics. 2011 Jan 15;27(2):270-1. doi: 10.1093/bioinformatics/btq636.

Getting started

  • The easiest way to install GimmeMotifs is using bioconda on Linux or Mac. From version 0.13.0 only Python 3 (>= 3.4) is supported.
  • Have a look at these simple examples to get a taste of what is possible.
  • Check out the more detailed tutorials.
  • Full command-line reference can be found here.
  • There’s also an API documentation.

Get help

  • First, check the FAQ for common issues.
  • The preferred way to get support is through the Github issues page.
  • Finally, you can reach me by mail or via twitter.