Short Dispersed Repeats

Short Dispersed Repeats KALEIGH, MARIAM, MICHAEL AND NICHOLAS

Start Associated Sequences in EnterobacteriophageKALEIGH HEDGES

Ribosomal Binding Site (Shine-Dalgarno)

http://themedicalbiochemistrypage.org/protein-synthesis.php#polya

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?

Biobike / MEME

Start Associated Sequences found in Enterobacterioophage

Full Length ERIC Sequence Occurrence in BacteriophageMICHAEL KIFLEZGHI

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)

Enterobacterial Repetitive Intergenic Consensus Sequences

Wilson L A , and Sharp P M Mol Biol Evol 2006;23:1156-1168

PhAnToMe/BioBIKE: detecting the imperfect palindrome

AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT

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AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGAGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT

Window

CACTTACTTGTGTA AGCTCCCGGAGGAT

TAGGAGGCCCTCGA

Reverse


AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGAGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT

Window

CACTTACTTGTGTA AGCTCCCGGAGGAT

TAGGAGGCCCTCGASCORE = 5

Preliminary Results

Sequence found in Enterobacteria Phage Lambda

Identification of Possible RNA Hairpin Sequences in sub-cluster B3Mycobacteriophages MARIAM SANKOH

How did I get here?

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

Sample Input and Output

Location Identification of Initial Sequences

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?

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

NICHOLAS RODRIGUEZ

Questions? Can new genes be created by transposable elements?

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

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

Proposed Mechanism

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

Selectively Sequenced msRNA

ERICSAATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT CATACCCTATGGATTTCTGGGTGCAGCAAGGTAGCAAGCGCCAGAATCCCCAGGAGCTTACATAAGTAAGTGACTGGGGTGAGGGCGTGAAGCTAACGCCGCTGCGGCCTGAAAGACGACGGGTATG CTCCCCCAAAATAGTTCGAGTTGCAGAAAGGCGGCAAGCTCGAGAATTCCCGGGAGCTTACATCAGTAAGTGACCGGGATGAGCGAGCGAAGATAACGCATCTGCGGCGCGAAATATGAAGGGGGAG TATACTCTAAATAATTCGAGTTGCAGGAAGGCGACAAGCGAGTGAATCGCCAGGAGCTTACATAAGTAAGTGACTGGGGTGAACGAACGCAGTCGCAGTACATGCAACTTGAAGTATGACGAGTATA TATACTCGTCATACTTCAAGTTGCATGTGCTGCGGCTGCATTCGTTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGCTTCACTCGTTTGCCGCCTTCCTGCAACTCGAATTATTTAGAGTCTA TATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATG TATTCTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATA TATACACAAAATCATTCAAGTTGCATCAAGGCGGCAAGTGAGCGAATCCCGATGAGCTTACTCAGGTAAGTGATTCGGGGGAGCGAACGCAGCCAAGGCAGAGGCGGCTTGAAGGATGAAGTGTATA TATACACTTTATCCTTCACGCTGCCTCTTCGTTGACTGCCTTCGCTCATCCCATTCACATAGTTATCTATGCTCATGGGAGTTCACTCAGTTGCCGCCTCGATGCAACGCGAATGATTTCGTGTATT TCCGCTAAATGATTCGCGTTGCAGGAAGGCGGCAAGTGAGTGAAGCCCCAGGAGCATAGATAACTATGTGACTGGGGTGAACGAGCGCAGCCAACGCATCTGCGGCGTGAAGCATGACGCGGAAATT TACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGAA CACCAGCTGTTTGCCCTGTACGGCATCGAAGCGACGCTGTTCATAACGCGGCGTAATACCGTTTTCTTCAGGCATGATCCAGATCTGATACAGATGCAGACGCTCGGTGCTGCTTGGGTTGTACTCT ATCGTAGTTAAAGACGTGCGTCACTGCCGGAATATGCAAACCACGCGCGGCAACGTCGGTGGCAACCAGAATATCCAGATCGCCACGGGTAAATTCATCAAGAATACGCAGACGTTTTTTCTGCGCG CCTGTTCCGTATTGGTCGTGGACGTGCGCCGACTGGCGAACCTGCGGCGGCAGCGGAAATGACCAAATGGTTTAACACCAACTATCACTACATGGTGCCGGAGTTCGTTAAAGGCCAACAGTTCAAA GTCTCTTTCCATGCTTTGCGCAGGGAAGATTCCTCAAAGTGCTGGCGGTCAAACCACTCCTGTAGCTCGACCAGCCCTTTACGGGTGAGATCGCGCGGGCGATTAATAACTGCCTGCAATGCCGGTT

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

msRNA in ERICsAATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT CATACCCTATGGATTTCTGGGTGCAGCAAGGTAGCAAGCGCCAGAATCCCCAGGAGCTTACATAAGTAAGTGACTGGGGTGAGGGCGTGAAGCTAACGCCGCTGCGGCCTGAAAGACGACGGGTATG CTCCCCCAAAATAGTTCGAGTTGCAGAAAGGCGGCAAGCTCGAGAATTCCCGGGAGCTTACATCAGTAAGTGACCGGGATGAGCGAGCGAAGATAACGCATCTGCGGCGCGAAATATGAAGGGGGAG TATACTCTAAATAATTCGAGTTGCAGGAAGGCGACAAGCGAGTGAATCGCCAGGAGCTTACATAAGTAAGTGACTGGGGTGAACGAACGCAGTCGCAGTACATGCAACTTGAAGTATGACGAGTATA TATACTCGTCATACTTCAAGTTGCATGTGCTGCGGCTGCATTCGTTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGCTTCACTCGTTTGCCGCCTTCCTGCAACTCGAATTATTTAGAGTCTA TATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATG TATTCTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATA TATACACAAAATCATTCAAGTTGCATCAAGGCGGCAAGTGAGCGAATCCCGATGAGCTTACTCAGGTAAGTGATTCGGGGGAGCGAACGCAGCCAAGGCAGAGGCGGCTTGAAGGATGAAGTGTATA TATACACTTTATCCTTCACGCTGCCTCTTCGTTGACTGCCTTCGCTCATCCCATTCACATAGTTATCTATGCTCATGGGAGTTCACTCAGTTGCCGCCTCGATGCAACGCGAATGATTTCGTGTATT TCCGCTAAATGATTCGCGTTGCAGGAAGGCGGCAAGTGAGTGAAGCCCCAGGAGCATAGATAACTATGTGACTGGGGTGAACGAGCGCAGCCAACGCATCTGCGGCGTGAAGCATGACGCGGAAATT TACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGAA CACCAGCTGTTTGCCCTGTACGGCATCGAAGCGACGCTGTTCATAACGCGGCGTAATACCGTTTTCTTCAGGCATGATCCAGATCTGATACAGATGCAGACGCTCGGTGCTGCTTGGGTTGTACTCT ATCGTAGTTAAAGACGTGCGTCACTGCCGGAATATGCAAACCACGCGCGGCAACGTCGGTGGCAACCAGAATATCCAGATCGCCACGGGTAAATTCATCAAGAATACGCAGACGTTTTTTCTGCGCG CCTGTTCCGTATTGGTCGTGGACGTGCGCCGACTGGCGAACCTGCGGCGGCAGCGGAAATGACCAAATGGTTTAACACCAACTATCACTACATGGTGCCGGAGTTCGTTAAAGGCCAACAGTTCAAA GTCTCTTTCCATGCTTTGCGCAGGGAAGATTCCTCAAAGTGCTGGCGGTCAAACCACTCCTGTAGCTCGACCAGCCCTTTACGGGTGAGATCGCGCGGGCGATTAATAACTGCCTGCAATGCCGGTT

Finding Motifs

Motifs

Motif 2 - 11bp

Random Motif 1 - 10bp


Random Motif - 2 9bp


0

2

4

6

8

10

12

14

16

18

Motifs Co-located from ERIC sequences and msRNA

Series1

Motifs Co-located from ERIC sequences and msRNA

Num

ber o

f Mat

ches

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

Documents

Short Dispersed Repeats