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Aliya Sadeque BIOC 599 Supervisory Committee Meeting

Aliya Sadeque BIOC 599 Supervisory Committee Meeting. Wednesday December 19, 2007. Outline. About me Thesis project blueprint Course selection. Curriculum Vitae. Queen’s University . Bachelor of Science (Honours) in Biochemistry. Minor in Computing. Graduated May, 2007.

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Aliya Sadeque BIOC 599 Supervisory Committee Meeting

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  1. Aliya SadequeBIOC 599Supervisory Committee Meeting Wednesday December 19, 2007.

  2. Outline • About me • Thesis project blueprint • Course selection

  3. Curriculum Vitae • Queen’s University.Bachelor of Science (Honours) in Biochemistry. Minor in Computing.Graduated May, 2007

  4. Previous Coursework • Undergraduate Level Biochemistry: • Proteins and Enzymes • Physical Biochemistry • Metabolism • Molecular Biology • Introductory Biochemistry Laboratory • Protein Structure and Function • Current Topics in Biochemistry • Biochemistry of the Cell • Advanced Molecular Biology

  5. Previous Coursework • Undergraduate Level Computing: • Database Management Systems • Neural and Genetic Computing • Introduction to Data Mining • System Level Programming • Operating Systems • Undergraduate Level Mathematics: • Introduction to Statistics • Discrete Math for Computer Scientists • Modeling Techniques in Biology

  6. Thesis Project Blueprint • Context • What do we know so far • Why is this work important • LCS • Hits curves • where does the number of hits explode • Visualization • Where are these regions • Further investigation of regions of interest • Promoter Prediction • Tools • Existing tools: what’s out there? • Developing a new tool • Visualization • visualize all predicted promoters against LCS identified regions

  7. Context • Promoter sequences might be identified as conserved islands in a divergent sea”

  8. Longest Common Subsequence

  9. Longest Common Subsequence

  10. Longest Common Subsequence • Hits Curves

  11. Longest Common Subsequence • Hits Curves

  12. Promoter Prediction • Existing Tools • Interpolated Context Modeling (ICM) • Feedforward Neural Network • New ideas for promoter prediction • Neural Networks • Drosophila tool • GPCR tool • Data mining techniques • WEKA • Other forms of computer learning

  13. Course Selection • BIOC 570 - completed • MICR 502 - Virology • Courses to sit in for: • Biochemistry courses? • Computing courses? • Data mining • Bioinformatics

  14. Questions for myself • Hits curves – what does it mean if they identify same region? • Exact to approximate matches • Why is this study important • What weka tools would be good?

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