Short Dispersed Repeats KALEIGH, MARIAM, MICHAEL AND NICHOLAS.

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Presentation transcript:

Short Dispersed Repeats KALEIGH, MARIAM, MICHAEL AND NICHOLAS

Start Associated Sequences in Enterobacteriopha ge KALEIGH HEDGES

Ribosomal Binding Site (Shine-Dalgarno)

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 Bacteriophage MICHAEL 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:

PhAnToMe/BioBIKE: detecting the imperfect palindrome AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCC GCCTTGCTCTGACGCGAAATACTTCGGAAATT Window

PhAnToMe/BioBIKE: detecting the imperfect palindrome AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCC GCCTTGCTCTGACGCGAAATACTTCGGAAATT Window

PhAnToMe/BioBIKE: detecting the imperfect palindrome AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCC GCCTTGCTCTGACGCGAAATACTTCGGAAATT Window

PhAnToMe/BioBIKE: detecting the imperfect palindrome AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCC GCCTTGCTCTGACGCGAAATACTTCGGAAATT Window

PhAnToMe/BioBIKE: detecting the imperfect palindrome AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCC GCCTTGCTCTGACGCGAAATACTTCGGAAATT Window

PhAnToMe/BioBIKE: detecting the imperfect palindrome AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCC GCCTTGCTCTGACGCGAAATACTTCGGAAATT Window

PhAnToMe/BioBIKE: detecting the imperfect palindrome AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCC GCCTTGCTCTGACGCGAAATACTTCGGAAATT Window

PhAnToMe/BioBIKE: detecting the imperfect palindrome AATTTCCTTCGTCTTTCACGCCATAGCGGCGTTGGCGTCGCCCGCTCACCCCGGTCACTTACTTGTGTAAGCTCCCGGGGATTCACAGGCTAGCC GCCTTGCTCTGACGCGAAATACTTCGGAAATT Window

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

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

Preliminary Results Sequence found in Enterobacteria Phage Lambda

Identification of Possible RNA Hairpin Sequences in sub- cluster B3 Mycobacteriophages 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

ERICS

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

msRNA in ERICs

Finding Motifs

Motifs

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