MIC/MBG 653 Advanced Molecular Genetics
Bioinformatics & Computational Genomics (Spring 2004)
Help in using Meme
Meme is a program that facilitates the discovery of motifs in nucleic acid and protein sequences. You can run Meme off the web from Meme-Central (University of California at San Diego), from our own Watson server, or from the Hercules server. There are pros and cons to each choice.

In brief:

Running Meme from the UCSD site Running Meme from the Watson server Running Meme from the Hercules server
  • Log in on Hercules
  • Upload the file
  • Type in the line similar to the one below:
         meme name-of-file -dna -mod zoops -nmotifs 6 > name-of-output-file.html
  • Notes on above: 
       * Use -dna if using DNA sequences or -protein if using protein sequences
       * Use -mod oops if you want Meme to find precisely one motif-hit per sequence
                -mod zoops if you want Meme to find either zer or one motif-hit per sequence
                -mod tcm if any number will do
       * Type after -nmotifs the number of motifs you want Meme to find
  • You won't be able to read the output file within Hercules. Instead, download it to your own computer and read it with your favorite Web browser
  • Contact me
      Jeff Elhai
      Life Sciences Building, Room 335