1. Copyright OpenHelix. No use or reproduction without express written consent1

2. Materials prepared by: Cynthia Foote, Ph.D. www.openhelix.com Updated: Q1 2011 Version 2 MEME Suite

3. Copyright OpenHelix. No use or reproduction without express written consent3 MEME Suite Agenda Introduction and Credits Discover Motifs Align and Search Motif Similarity and GO Association Summary Exercises MEME: http://meme.sdsc.edu/

4. Copyright OpenHelix. No use or reproduction without express written consent4 Introduction Suite of Motif-based Sequence Analysis Tools Submit A Job

5. Copyright OpenHelix. No use or reproduction without express written consent5 What is a Motif? a pattern found repeatedly in DNA or protein sequences that may have biological significance. Frequently found motif: Slight differences in a motif can have important implications for function Zinc finger motif DNA binding C2H2 type RNA binding C2H2, CCHC and CCCH Protein binding LIM, MYND,RING and PHD

6. Copyright OpenHelix. No use or reproduction without express written consent6 ENCODE Project Current focus of human genome research is to find and catalog all the functional elements in the human genome sequence One type of important functional elements in human genome are motifs Ability to “discover” motifs an important component of ENCODE project

7. Copyright OpenHelix. No use or reproduction without express written consent7 Credits Authors: Timothy Bailey - University of Queensland William Stafford Noble - University of Washington Additional Input from: Charles Elkan Michael Gribskov Developed and Maintained by: Funded by the National Center for Research Resources grant NIH/NCRR R01 RR021692

8. Copyright OpenHelix. No use or reproduction without express written consent8 Publications http://nar.oxfordjournals.org/content/37/suppl_2/W202.long

9. Copyright OpenHelix. No use or reproduction without express written consent9 MEME Suite Agenda Introduction and Credits Discover Motifs Align and Search Motif Similarity and GO Association Summary Exercises MEME: http://meme.sdsc.edu/

10. Copyright OpenHelix. No use or reproduction without express written consent10 Discover Motifs Algorithm to discover non-gapped motifs in protein or DNA sequences Algorithm to discover gapped motifs in protein or DNA sequences

11. Copyright OpenHelix. No use or reproduction without express written consent11 Submitting Data to MEME http://meme.sdsc.edu/meme/cgi-bin/meme.cgi The preferred sequence format is FASTA, but others accepted Click here

12. Copyright OpenHelix. No use or reproduction without express written consent12 Results Overview Report sections Overview followed by individual motif details Focus here next slide Combined block diagrams Program information Explanation of terminology in report

13. Copyright OpenHelix. No use or reproduction without express written consent13 Understanding the Results - Motif 1 Regular expression Further Analysis of motif 1 Standard or Reverse Complement Further Analysis of all motifs

14. Copyright OpenHelix. No use or reproduction without express written consent14 Understanding the Results - Motif 1, Lower Data Formats Sites Block Diagrams for motif 1 Block Diagrams for all motifs

15. Copyright OpenHelix. No use or reproduction without express written consent15 GLAM2 Required Parameters Enter sequence Enter email Edit options Start search

16. Copyright OpenHelix. No use or reproduction without express written consent16 GLAM2 Results Page

17. Copyright OpenHelix. No use or reproduction without express written consent17 MEME Suite Agenda Introduction and Credits Discover Motifs Align and Search Motif Similarity and GO Association Summary Exercises MEME: http://meme.sdsc.edu/

18. Copyright OpenHelix. No use or reproduction without express written consent18 Align and Search Finds additional occurrences of motif Finds individual motif occurrences Finds clusters of motifs Finds occurrences of gapped motifs

19. Copyright OpenHelix. No use or reproduction without express written consent19 MAST from MEME Results Click here

20. Copyright OpenHelix. No use or reproduction without express written consent20 MAST Results - Overview Report sections Mouse over Click arrow Drag over

21. Copyright OpenHelix. No use or reproduction without express written consent21 MAST Results - Additional Information

22. Copyright OpenHelix. No use or reproduction without express written consent22 FIMO from MEME Results Click here

23. Copyright OpenHelix. No use or reproduction without express written consent23 FIMO Results Report sections Sequence name, position, & scores

24. Copyright OpenHelix. No use or reproduction without express written consent24 MCAST - Data Submission Click here Categories Databases FASTA file

25. Copyright OpenHelix. No use or reproduction without express written consent25 MCAST Results Report sections Displays ID, E-value, score, hits, location & description

26. Copyright OpenHelix. No use or reproduction without express written consent26 MCAST Results - More Information Input motif Matched sequence

27. Copyright OpenHelix. No use or reproduction without express written consent27 GLAM2SCAN from GLAM2 Results Click here

28. Copyright OpenHelix. No use or reproduction without express written consent28 GLAM2SCAN Results List of sequence matches with scores Display of motif site, with start and end points List of Sequence Matches

29. Copyright OpenHelix. No use or reproduction without express written consent29 MEME Suite Agenda Introduction and Credits Discover Motifs Align and Search Motif Similarity and GO Association Summary Exercises MEME: http://meme.sdsc.edu/

30. Copyright OpenHelix. No use or reproduction without express written consent30 TOMTOM Compares DNA motifs against databases of known motifs

31. Copyright OpenHelix. No use or reproduction without express written consent31 TOMTOM from MEME Results Click here

32. Copyright OpenHelix. No use or reproduction without express written consent32 TOMTOM Results Report sections LOGO of Match LOGO of Query Next Match Create custom LOGO Motif Report

33. Click here Copyright OpenHelix. No use or reproduction without express written consent33 GOMO - Gene Ontology for Motifs Or begin here

34. Report sections Copyright OpenHelix. No use or reproduction without express written consent34 GOMO Results GO terms associated with putative gene targets Ranked Genes

35. Copyright OpenHelix. No use or reproduction without express written consent35 MEME Suite Agenda Introduction and Credits Discover Motifs Align and Search Motif Similarity and GO Association Summary Exercises MEME: http://meme.sdsc.edu/

36. Copyright OpenHelix. No use or reproduction without express written consent36 MEME Suite Summary

37. Copyright OpenHelix. No use or reproduction without express written consent37 MEME Suite Agenda Introduction and Credits Discover Motifs Align and Search Motif Similarity and GO Association Summary Exercises MEME: http://meme.sdsc.edu/

38. Copyright OpenHelix. No use or reproduction without express written consent38