1. Short Dispersed Repeats KALEIGH, MARIAM, MICHAEL AND NICHOLAS

2. Start Associated Sequences in Enterobacteriopha ge KALEIGH HEDGES

3. Ribosomal Binding Site (Shine-Dalgarno) http://themedicalbiochemistrypage.org/protein-synthesis.php#polya

5. Is there a conserved sequence in Enterobacteriophage that could help support translation initiation? Where are these repeats located? How far away from Gene start? What is the associated start codon? Do the sequences contain the Shine-Dalgarno sequence or is it nearby?

6. Biobike / MEME

7. Start Associated Sequences found in Enterobacterioophage

8. Full Length ERIC Sequence Occurrence in Bacteriophage MICHAEL KIFLEZGHI

9. Question: Do Bacteriophage contain ERIC sequences? Some Bacteriophage have potential (and in some cases realized) clinical applications (1) Bacteriophage sometimes acquire host DNA (2, 3)

10. Enterobacterial Repetitive Intergenic Consensus Sequences Wilson L A, and Sharp P M Mol Biol Evol 2006;23:1156-1168

11. PhAnToMe/BioBIKE: detecting the imperfect palindrome AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCC GCCTTGCTCTGACGCGAAATACTTCGGAAATT Window

12. PhAnToMe/BioBIKE: detecting the imperfect palindrome AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCC GCCTTGCTCTGACGCGAAATACTTCGGAAATT Window

13. PhAnToMe/BioBIKE: detecting the imperfect palindrome AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCC GCCTTGCTCTGACGCGAAATACTTCGGAAATT Window

14. PhAnToMe/BioBIKE: detecting the imperfect palindrome AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCC GCCTTGCTCTGACGCGAAATACTTCGGAAATT Window

15. PhAnToMe/BioBIKE: detecting the imperfect palindrome AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCC GCCTTGCTCTGACGCGAAATACTTCGGAAATT Window

16. PhAnToMe/BioBIKE: detecting the imperfect palindrome AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCC GCCTTGCTCTGACGCGAAATACTTCGGAAATT Window

17. PhAnToMe/BioBIKE: detecting the imperfect palindrome AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCC GCCTTGCTCTGACGCGAAATACTTCGGAAATT Window

18. PhAnToMe/BioBIKE: detecting the imperfect palindrome AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCC GCCTTGCTCTGACGCGAAATACTTCGGAAATT Window

19. PhAnToMe/BioBIKE: detecting the imperfect palindrome AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGAGGATTCACAGGCTAGCC GCCTTGCTCTGACGCGAAATACTTCGGAAATT Window CACTTACTTGTGTAAGCTCCCGGAGGAT TAGGAGGCCCTCGA Reverse

20. PhAnToMe/BioBIKE: detecting the imperfect palindrome AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGAGGATTCACAGGCTAGCC GCCTTGCTCTGACGCGAAATACTTCGGAAATT Window CACTTACTTGTGTAAGCTCCCGGAGGAT TAGGAGGCCCTCGA SCORE = 5

21. Preliminary Results Sequence found in Enterobacteria Phage Lambda

22. Identification of Possible RNA Hairpin Sequences in sub- cluster B3 Mycobacteriophages MARIAM SANKOH

23. How did I get here?

24. Where did I go from there? Inputs Sequence Number of Mismatches Organism Display Context of Coordinate 1 Coordinate 2 Alignment of Real Sequence with its reverse complement Plain Sequence

25. Sample Input and Output

26. Location Identification of Initial Sequences

27. PALINDROMES WITHIN GENES Decrease Function Runtime Decrease Noise and Repeats Allow User to Expand Window Size ◦Grab upstream and downstream sequence Confirm Repeated Sequences Function determination of Hairpin Sequences IMPROVEMENTS TO FUNCTION What’s Next?

28. Identification of Small Regulatory RNA within Miniature Inverse- Repeat Elements of E. Coli K-12 NICHOLAS RODRIGUEZ

29. Questions? Can new genes be created by transposable elements?

30. Questions? Can an organism make use of new genes in an advantageous way?

31. Small Regulator y RNA Short ~19-25bp Palindromes Regulate gene expression?

32. Proposed Mechanism

33. Identification of microRNA- Size, Small RNAs in Escherichia coli. Kang et al 2013 Selectively Sequenced msRNA

34. ERICS

35. Methods Searched for msRNAs in ERICs Located Motifs from ERICSs in msRNA

36. msRNA in ERICs

37. Finding Motifs

38. Motifs

39. Where are the msRNA? Near highly expressed genes Hitching a ride?