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Final Project

Final Project. Select One. Sequencing Program Re-organize read data Incorporate oligomer statistics Epigenetic study Obtain epigenetic data Protein Structure Finding internally symmetric structure in proteins. Sequencing. Newer illumina read data gets longer 150 to 300 bp per read

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Final Project

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  1. Final Project

  2. Select One • Sequencing Program • Re-organize read data • Incorporate oligomer statistics • Epigenetic study • Obtain epigenetic data • Protein Structure • Finding internally symmetric structure in proteins

  3. Sequencing • Newer illumina read data gets longer • 150 to 300 bp per read • De Bruijn approach may not be suitable for longer reads • Segment each read to multiple k-mers sliding by one base from a read • K=27 • May lose info from k-mers to reads • Brute-force OLC is NP-complete

  4. Sequencing 2 • OLC with data partition • Front bins of identical first k-mers of reads • Rear bins of identical last k-mers of reads • K=15, 415 = 230 = 1 billion bins* 2 • Join F and R bins with the same k-mers • Produce consensus contigs with bp matches over a threshold • Repeat generating new F & R bins, • Each time dealing with longer contigs • Per-bucket sequencing

  5. Sequencing 3 • Is this a valid approach ? • Analysis in time and space, any advantage vs. conventional OLC ? • Implementation in any language • 2 Yeast chromosomes • when reads from both are mixed, can they be separated • 16 Yeast chromosomes • Each contig > 100 Kbp should have the same oligomer % distribution as the one from the genome • Delete contigs not matching oligomer distribution

  6. Epigenetic Study • www.cs.uml.edu/~kim/epi_disease.pdf • Epigenetic evidences in cancer, Altzheimer, neurological disorder, obesity, etc. • Select one chapter on human diseases • Obtain epigenetic data • Reproduce the results

  7. Protein Structure • www.cs.uml.edu/~kim/symD_article.pdf • symD.pdf paper describes the algorithm for finding symmetric structure in a protein and its results. • Program that performed the analysis is available in www.cs.uml.edu/~kim/580/symd1.0.tar • Use symmD.zip program (in C), and reproduce the results in the paper • If you want to extend the problem to finding ‘similar’ structures (not identical), describe which part of symd10.tar program needs to be modified and how.

  8. Schedule • Next class (4/7) • Hand in • Which topic you will work on • 4/28 (Mon) • 10-min presentation • No fancy power points • Due on 5/5 (Mon)

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