For this recipe, we need the datasets/ch3/simple_motif.txt and datasets/ch3/promoters.fa files, a simple matrix describing a simple motif in a Position Specific Weight Matrix (PSWM) format (see Appendix for a brief description), and a set of sequences from upstream of transcriptional start sites.

This recipe also requires a working copy of MEME on your system. MEME is a program for finding statistically overrepresented sequence motifs in sets of sequences. When used on promoter or upstream gene regions, these motifs can represent transcription factor-binding sites. The web page for MEME is at http://alternate.meme-suite.org/ and if you have conda installed, you can install it with conda install -c bioconda meme. The MEME package isn't available for Windows systems. If you wish to run it on Windows, then you should look at running it under Cygwin—a Linux emulation layer (https://www.cygwin.com/). You may need to install a new version of R under Cygwin as well.