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Bioinformatics

Bioinformatics. Prof. William Stafford Noble Department of Genome Sciences Department of Computer Science and Engineering University of Washington thabangh@gmail.com. Outline. Introductions Biology background Rosalind Sequence alignment. Washington state. 2,763 miles. Washington, DC.

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Bioinformatics

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  1. Bioinformatics Prof. William Stafford Noble Department of Genome SciencesDepartment of Computer Science and Engineering University of Washington thabangh@gmail.com

  2. Outline • Introductions • Biology background • Rosalind • Sequence alignment

  3. Washington state 2,763 miles Washington, DC

  4. Scout Nan Jack

  5. Introductory survey • p-value • t test • BLAST • Python sys.argv • support vector machine • false discovery rate • dynamic programming • recursion • hierarchical clustering • Wilcoxon test • Python tuple • Smith-Waterman • Bonferroni correction • Python dictionary Next to each concept, please enter 1, 2 or 3, as follows: I do not know this concept. I have heard of this concept, but could not give a precise definition. I know this concept well. Do not sign your name.

  6. On the index card, write • Your name • Your email address • Your home country • The year and subject of your bachelors degree • The name of your favorite undergraduate course • Your proficiency (introductory, intermediate, advanced) in Python, linear algebra, statistics, and biology • An interesting thing you have done • One question for me

  7. Name: Bill Noble • Email: thabangh@gmail.com • Country: United States • Degree: 1991 Symbolic Systems • Favorite course: Programming Methodology • Python: advanced • Statistics: advanced • Biology: intermediate • Interesting thing I have done: unicycling • Question: …

  8. Course goals By the end of this course, you should be able to This course will not Teach molecular biology techniques. Teach you how to use off-the-shelf bioinformatics software. • Describe some basic computational challenges in bioinformatics. • Implement and use several basic algorithms in this field. • Describe several advanced algorithms.

  9. What is life? • Entropy: the tendency toward disorder. • Living organisms have low entropy. • Soil has high entropy.

  10. The cell • Primary low entropy compartment • Tasks: • Gather energy • Maintain inside/outside distinction • Strategies: • Movement • Signal transduction • Energy capture • Reproduction

  11. Biological macromolecules • Lipids (fat): • membranes • energy storage • Carbohydrates (sugar): • energy storage • structure • cell-cell communication • Nucleic aids • genetic material • Proteins • workhorses of the cell

  12. The central dogma of molecular biology DNA Transcription RNA lejeuneusa.org Translation Protein Video rcsb.org

  13. 4-letter DNA alphabet • DNA consists of an alphabet of four bases • Adenine • Cytosine • Guanine • Thymine

  14. Rosalind • Visit http://rosalind.info and create a login. • Enroll in this class via http://rosalind.info/classes/enroll/e7948c7e32/ • Solve the problem, “Installing Python” • Solve the problem, “Counting DNA nucleotides.”

  15. Reverse complement T C TCAGG TCAGGTCACAGTT A Write down the rest of the DNA sequence. G G AAC AACTGTGACCTGA Write down the sequence you get by reading from the blue strand, starting at the bottom.

  16. Reverse complement TCAGGTCACAGTT ||||||||||||| AACTGTGACCTGA Rosalind: Complementing a strand of DNA

  17. One-minute response At the end of each class • Write for about one minute. • Provide feedback about the class. • Was part of the lecture unclear? • What did you like about the class? • Do you have unanswered questions? • Sign your name I will begin the next class by responding to the one-minute responses

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