short dispersed repeats kaleigh, mariam, michael and nicholas
TRANSCRIPT
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?
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
Window
PhAnToMe/BioBIKE: detecting the imperfect palindrome
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT
Window
PhAnToMe/BioBIKE: detecting the imperfect palindrome
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT
Window
PhAnToMe/BioBIKE: detecting the imperfect palindrome
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT
Window
PhAnToMe/BioBIKE: detecting the imperfect palindrome
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT
Window
PhAnToMe/BioBIKE: detecting the imperfect palindrome
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT
Window
PhAnToMe/BioBIKE: detecting the imperfect palindrome
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT
Window
PhAnToMe/BioBIKE: detecting the imperfect palindrome
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT
Window
PhAnToMe/BioBIKE: detecting the imperfect palindrome
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGAGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT
Window
CACTTACTTGTGTA AGCTCCCGGAGGAT
TAGGAGGCCCTCGA
Reverse
PhAnToMe/BioBIKE: detecting the imperfect palindrome
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGAGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT
Window
CACTTACTTGTGTA AGCTCCCGGAGGAT
TAGGAGGCCCTCGASCORE = 5
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
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
Identification of microRNA-Size, Small RNAs in Escherichia coli. Kang et al 2013
Selectively Sequenced msRNA
ERICS
AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT CATACCCTATGGATTTCTGGGTGCAGCAAGGTAGCAAGCGCCAGAATCCCCAGGAGCTTACATAAGTAAGTGACTGGGGTGAGGGCGTGAAGCTAACGCCGCTGCGGCCTGAAAGACGACGGGTATG CTCCCCCAAAATAGTTCGAGTTGCAGAAAGGCGGCAAGCTCGAGAATTCCCGGGAGCTTACATCAGTAAGTGACCGGGATGAGCGAGCGAAGATAACGCATCTGCGGCGCGAAATATGAAGGGGGAG TATACTCTAAATAATTCGAGTTGCAGGAAGGCGACAAGCGAGTGAATCGCCAGGAGCTTACATAAGTAAGTGACTGGGGTGAACGAACGCAGTCGCAGTACATGCAACTTGAAGTATGACGAGTATA TATACTCGTCATACTTCAAGTTGCATGTGCTGCGGCTGCATTCGTTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGCTTCACTCGTTTGCCGCCTTCCTGCAACTCGAATTATTTAGAGTCTA TATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATG TATTCTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATA TATACACAAAATCATTCAAGTTGCATCAAGGCGGCAAGTGAGCGAATCCCGATGAGCTTACTCAGGTAAGTGATTCGGGGGAGCGAACGCAGCCAAGGCAGAGGCGGCTTGAAGGATGAAGTGTATA TATACACTTTATCCTTCACGCTGCCTCTTCGTTGACTGCCTTCGCTCATCCCATTCACATAGTTATCTATGCTCATGGGAGTTCACTCAGTTGCCGCCTCGATGCAACGCGAATGATTTCGTGTATT TCCGCTAAATGATTCGCGTTGCAGGAAGGCGGCAAGTGAGTGAAGCCCCAGGAGCATAGATAACTATGTGACTGGGGTGAACGAGCGCAGCCAACGCATCTGCGGCGTGAAGCATGACGCGGAAATT TACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGAA CACCAGCTGTTTGCCCTGTACGGCATCGAAGCGACGCTGTTCATAACGCGGCGTAATACCGTTTTCTTCAGGCATGATCCAGATCTGATACAGATGCAGACGCTCGGTGCTGCTTGGGTTGTACTCT ATCGTAGTTAAAGACGTGCGTCACTGCCGGAATATGCAAACCACGCGCGGCAACGTCGGTGGCAACCAGAATATCCAGATCGCCACGGGTAAATTCATCAAGAATACGCAGACGTTTTTTCTGCGCG CCTGTTCCGTATTGGTCGTGGACGTGCGCCGACTGGCGAACCTGCGGCGGCAGCGGAAATGACCAAATGGTTTAACACCAACTATCACTACATGGTGCCGGAGTTCGTTAAAGGCCAACAGTTCAAA GTCTCTTTCCATGCTTTGCGCAGGGAAGATTCCTCAAAGTGCTGGCGGTCAAACCACTCCTGTAGCTCGACCAGCCCTTTACGGGTGAGATCGCGCGGGCGATTAATAACTGCCTGCAATGCCGGTT
msRNA in ERICsAATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCCGCCTTGCTCTGACGCGAAATACTTCGGAAATT CATACCCTATGGATTTCTGGGTGCAGCAAGGTAGCAAGCGCCAGAATCCCCAGGAGCTTACATAAGTAAGTGACTGGGGTGAGGGCGTGAAGCTAACGCCGCTGCGGCCTGAAAGACGACGGGTATG CTCCCCCAAAATAGTTCGAGTTGCAGAAAGGCGGCAAGCTCGAGAATTCCCGGGAGCTTACATCAGTAAGTGACCGGGATGAGCGAGCGAAGATAACGCATCTGCGGCGCGAAATATGAAGGGGGAG TATACTCTAAATAATTCGAGTTGCAGGAAGGCGACAAGCGAGTGAATCGCCAGGAGCTTACATAAGTAAGTGACTGGGGTGAACGAACGCAGTCGCAGTACATGCAACTTGAAGTATGACGAGTATA TATACTCGTCATACTTCAAGTTGCATGTGCTGCGGCTGCATTCGTTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGCTTCACTCGTTTGCCGCCTTCCTGCAACTCGAATTATTTAGAGTCTA TATACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATG TATTCTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCGCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATA TATACACAAAATCATTCAAGTTGCATCAAGGCGGCAAGTGAGCGAATCCCGATGAGCTTACTCAGGTAAGTGATTCGGGGGAGCGAACGCAGCCAAGGCAGAGGCGGCTTGAAGGATGAAGTGTATA TATACACTTTATCCTTCACGCTGCCTCTTCGTTGACTGCCTTCGCTCATCCCATTCACATAGTTATCTATGCTCATGGGAGTTCACTCAGTTGCCGCCTCGATGCAACGCGAATGATTTCGTGTATT TCCGCTAAATGATTCGCGTTGCAGGAAGGCGGCAAGTGAGTGAAGCCCCAGGAGCATAGATAACTATGTGACTGGGGTGAACGAGCGCAGCCAACGCATCTGCGGCGTGAAGCATGACGCGGAAATT TACTCGTCATACTTCAAGTTGCATGTGCTGCGTCTGCGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTCCTGGGGATTCACTCTCTTGTCGCCTTCCTGCAACTCGAATTATTTAGAGTATGAA CACCAGCTGTTTGCCCTGTACGGCATCGAAGCGACGCTGTTCATAACGCGGCGTAATACCGTTTTCTTCAGGCATGATCCAGATCTGATACAGATGCAGACGCTCGGTGCTGCTTGGGTTGTACTCT ATCGTAGTTAAAGACGTGCGTCACTGCCGGAATATGCAAACCACGCGCGGCAACGTCGGTGGCAACCAGAATATCCAGATCGCCACGGGTAAATTCATCAAGAATACGCAGACGTTTTTTCTGCGCG CCTGTTCCGTATTGGTCGTGGACGTGCGCCGACTGGCGAACCTGCGGCGGCAGCGGAAATGACCAAATGGTTTAACACCAACTATCACTACATGGTGCCGGAGTTCGTTAAAGGCCAACAGTTCAAA GTCTCTTTCCATGCTTTGCGCAGGGAAGATTCCTCAAAGTGCTGGCGGTCAAACCACTCCTGTAGCTCGACCAGCCCTTTACGGGTGAGATCGCGCGGGCGATTAATAACTGCCTGCAATGCCGGTT
Motifs
Motif 2 - 11bp
Random Motif 1 - 10bp
Random Motif 2 - 10bp
Random Motif - 2 9bp
Random Motif 3 - 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
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f Mat
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