1 / 21

Bioinformatics

This course, led by Prof. William Stafford Noble from the University of Washington, offers an introduction to bioinformatics, focusing on computational approaches in biology. Key topics include basic and advanced computational challenges, sequence alignment, and established algorithms such as BLAST, Smith-Waterman, and support vector machines. Students will engage with bioinformatics software, implementing algorithms using Python. The course aims to foster a deep understanding of biological macromolecules, the central dogma, and the principles of entropy in living systems.

summer
Télécharger la présentation

Bioinformatics

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related