1. CSE 5290: Algorithms for Bioinformatics Fall 2009
Suprakash Datta
Office: CSEB 3043
Phone: ext 77875
Course page:
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CSE 5290, Fall 2009

2. My research Computer Networks….. Clustering of Biological data, e.g.
Flow cytometry data
Microarray data
Genomic Signal Processing
Convert biological sequences to numerical sequences and apply signal processing tools
exon prediction, retroviral insertions
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CSE 5290, Fall 2009

3. Administrivia Lectures: Tue-THu 1:00 - 2:30 pm (Ross S 537)
Textbook:
Lectures: Tue-THu 1:00 - 2:30 pm (Ross S 537)
Office hours: Wed 1-4 pm, or by appointment.
TA: none.
Webpage: All announcements/handouts will be published on the webpage -- check often for updates)
An Introduction to Bioinformatics Algorithms Neil C. Jones and Pavel A. Pevzner MIT Press, August 2004.
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4. Administrivia – contd. Described in more detail on webpage Grading:
Midterms : 30%
Homework : 30%
Project: 40%
Grades: will be on ePost.
Project details are on the webpage.
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CSE 5290, Fall 2009

5. Course objectives Familiarity with computational problems in Biology
Applying algorithmic ideas
Understand real-life computational challenges
Improve understanding of algorithms
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CSE 5290, Fall 2009

6. What I expect from you Some familiarity with undergraduate algorithms
Interest in computational problems
Willingness to pick up a little Biology
Active interest in your project and assignments
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CSE 5290, Fall 2009

7. What is bioinformatics?
No consensus!
Genomics
Proteomics
Evolutionary biology
Clinical trial informatics
Epidemiology?
Medical image processing?
Artificial life?
From
“Bioinformatics is the field of science in which biology, computer science, and information technology merge to form a single discipline.”
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8. Why Bioinformatics? Make an impact! Interdisciplinary work
Work with real data sets
Use algorithmic skills
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9. Biological (genomic) data
ATATTGAATTTTCAAAAATTCTTACTTTTTTTTTGGATGGACGCAAAGAAGTTTAATAATCATATTACATGGCATTACCACCATATATATCCATATCTAATCTTACTTATATGTTGTGGAAATGTAAAGAGCCCCATTATCTTAGCCTAAAAAAACCTTCTCTTTGGAACTTTCTAATACGCTTAACTGCTCATTGCTATATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCGACAGCCCTCCGACGGAAGACTCTCCTCTGCGTCCTCGTCTTCACCGGTCGCGTTCCTGAAACGCAGATGTGCCTCGCGCCGCACTGCTCCGAACAATAAAGATTCTACAATACTCTTTTATGGTTATGAAGAGGAAAAATTGGCAGTAACCTGGCCCCACAAACCTTCAAATTAACGAATCAAATTAACAACCATAGGATGAATGCGATTAGTTTTTTAGCCTTATTTCTGGGGTAATTAATCAGCGAAGCGATGATTTTTGATCTATTAACAGATATATAAATGGAAGCTGCATAACCACTTTAACTAATACTTTCAACATTTTCAGTTTGTATTACTTCTTATTCAAATGTCATAAAAGTATCAACAAAAAATTTAATATACCTCTATACTTTAACGTCAAGGAGAAAAAACTATAATGACTAAATCTCATTCAGAAGAAGTGATTGTACCTGAGTTCAACTAGCGCAAAGGAATTACCAAGACCATTGGCCGAAAAGTGCCCGAGCATAATTAAGAAATTTATAAGCGCTTATGATGCTAAACCGGTTTGTTGCTAGATCGCCTGGTAGAGTCAATCTAATTGGTGAACATATTGATTATTGTGACTTCTCGGTTTTACCTTTAGCTATTGATTGATATGCTTTGCGCCGTCAAAGTTTTGAACGAGAAAAATCCATCCATTACCTTAATAAATGCTGATCCCAAATTTGCTCAAAGGAATCGATTTGCCGTTGGACGGTTCTTATGTCACAATTGATCCTTCTGTGTCGGACTGGTCTAATTACTTTAAATGTGGTCTCCATGTTGCACTCTTTTCTAAAGAAACTTGCACCGGAAAGGTTTGCCAGTGCTCCTCTGGCCGGGCTGCAAGTCTTCTGTGAGGGTGATGTACCATGGCAGTGATTGTCTTCTTCGGCCGCATTCATTTGTGCCGTTGCTTTAGCTGTTGTTAAAGCGAATATGGGCCCTGGTTATCATATCCAAGCAAAATTTAATGCGTATTACGGTCGTTGCAGAACATTATGTTGGTGTTAACAATGGCGGTATGGATCAGGCTGCCTCTGTTTGGTGAGGAAGATCATGCTCTATACGTTGAGTTCAAACCGCAGTTGAAGGCTACTCCGTTTAAATTTCCGCAATTAAAAAACCATGAATAGCTTTGTTATTGCGAACACCCTTGTTGTATCTAACAAGTTTGAAACCGCCCCAACCAACTATAATTTAAGAGTGGTAGAAGTCACCAGCTGCAAATGTTTTAGCTGCCACGTACGGTGTTGTTTTACTTTCTGGAAAAGAAGGATCGAGCACGAATAAAGGTAATCTAAGAGTTCATGAACGTTTATTATGCCAGATATCACAACATTTCCACACCCTGGAACGGCGATATTGAATCCGGCATCGAACGGTTAACAAAGGCTAGTACTAGTTGAAGAGTCTCTCGCCAATAAGAAACAGGGCTTTAGTGTTGACGATGTCGCACAATCCTTGAATTGTTCTCGCGAAATTCACAAGAGACTACTTAACAACATCTCCAGTGAGATTTCAAGTCTTAAAGCTATATCAGAGGGCTAAGCATGTGTATTCTGAATTTAAGAGTCTTGAAGGCTGTGAAATTAATGACTACAGCGAGCTTTACTGCCGACGAAGACTTTTTCAAGCAATTTGGTGCCTTGATGCGAGTCTCAAGCTTCTTGCGATAAACTTTACGAATGTTCTTGTCCAGAGATTGACAAAATTTGTTCCATTGCTTTGTCAAATGGATCATGGTTCCCGTTTGACCGGAGCTGGCTGGGGTGGTTGTACTGTTCACTTGGTTCCAGGGGGCCCAAATGGCAACATAGAAAAGGTAAGAAGCCCTTGCCAATGAGTTCTACAAGGTCAAGTACCCTAAGATCACTGATGCTGAGCTAGAAAATGCTATCATCGTCTCTAAACCAATTGGGCAGCTGTCTATATGAATTATAAGTATACTTCTTTTTTTTACTTTGTTCAGAACAACTTCTCATTTTTTTCTACTCATAACTAGCATCACAAAATACGCAATAATAACGAGTAGTAACACTTTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAGTTTTCAATGTAAGAGATTTCGATTATCCACAAACTTTAAAACACAGGGACAAAATTCTTGATATGCTTTCAACCGCTGCGTTTTGGACCTATTCTTGACATGATATGACTACCATTTTGTTATTGTACGTGGGGCAGTTGACGTCTTATCATATGTCAAAGTCATTTGCGAAGCTTGGCAAGTTGCCAACTGACGAGATGCAGTAAAAAGAGATTGCCGTCTTGAAACTTTTTGTCCTTTTTTTTTTCCGGGGACTCTACGAACCCTTTGTCCTACTGATTAATTTTGTACTGAATTTGGACAATTCAGATTTTAGTAGACAAGCGCGAGGAGGAAAAGAAATGACAAAAATTCCGATGGACAAGAAGATAGGAAAAAAAAAAAGCTTTCACCGATTTCCTAGACCGGAAAAAAGTCGTATGACATCAGAATGAAATTTTCAAGTTAGACAAGGACAAAATCAGGACAAATTGTAAAGATATAATAAACTATTTGATTCAGCGCCAATTTGCCCTTTTCCATTCCATTAAATCTCTGTTCTCTCTTACTTATATGATGATTAGGTATCATCTGTATAAAACTCCTTTCTTAATTTCACTCTAAAGCATCCCATAGAGAAGATCTTTCGGTTCGAAGACATTCCTACGCATAATAAGAATAGGAGGGAATAATGCCAGACAATCTATCATTACATTAGCGGCTCTTCAAAAAGATTGAACTCTCGCCAACTTATGGAATCTTCCAATGAGACCTTTGCGCCAAATAATGTGGATTTGGAAAAAGTATAAGTCATCTCAGAGTAATATAACTACCGAAGTTTATGAGGCATCGAGCTTTGAAGAAAAAGTAAGCTCAGAAAAACCTCAATAGCTCATTCTGGAAGAAAATCTATTATGAATATGTGGTCGTTGACAAATCAATCTTGGGTGTTTCTATTCTGGATTCATTTATGTACACAGGACTTGAAGCCCGTCGAAAAAGAAAGGCGGGTTTGGTCCTGGTACAATTATTGTTACTTCTGGCTTGCTGAATGTTTCAATATCCACTTGGCAAATTGCAGCTACAGGTCTACAACTGGGTCTAAATTGGTGGCAGTGTTGGATAACAATTTGGATTGGGTACGGTTTCGTGTGCTTTTGTTGTTTTGGCCTCTAGAGTTGGATCTGCTTATCATTTGTCATTCCCTATATCATCTAGAGCATCATTCGGTATTTTCT
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CSE 5290, Fall 2009

10. Annotated data 4/29/2019 CSE 5290, Fall 2009
ATATTGAATTTTCAAAAATTCTTACTTTTTTTTTGGATGGACGCAAAGAAGTTTAATAATCATATTACATGGCATTACCACCATATATATCCATATCTAATCTTACTTATATGTTGTGGAAATGTAAAGAGCCCCATTATCTTAGCCTAAAAAAACCTTCTCTTTGGAACTTTCTAATACGCTTAACTGCTCATTGCTATATTGAAGTACGGATTAGAAGCCGCCGAGCGGGCGACAGCCCTCCGACGGAAGACTCTCCTCTGCGTCCTCGTCTTCACCGGTCGCGTTCCTGAAACGCAGATGTGCCTCGCGCCGCACTGCTCCGAACAATAAAGATTCTACAATACTCTTTTATGGTTATGAAGAGGAAAAATTGGCAGTAACCTGGCCCCACAAACCTTCAAATTAACGAATCAAATTAACAACCATAGGATGAATGCGATTAGTTTTTTAGCCTTATTTCTGGGGTAATTAATCAGCGAAGCGATGATTTTTGATCTATTAACAGATATATAAATGGAAGCTGCATAACCACTTTAACTAATACTTTCAACATTTTCAGTTTGTATTACTTCTTATTCAAATGTCATAAAAGTATCAACAAAAAATTTAATATACCTCTATACTTTAACGTCAAGGAGAAAAAACTATAATGACTAAATCTCATTCAGAAGAAGTGATTGTACCTGAGTTCACTAGCGCAAAGGAATTACCAAGACCATTGGCCGAAAAGTGCCGAGCATAATTAAGAAATTTATAAGCGCTTATGATGCTAAACCGAGTTGTATGTATTTGGCCTTATGTAGCTCGCGCCCGTTCGAGATAAGGATGTTTCTAGAAATCCGTAAAGATATAGAGATGTACACACATCTACATTTGTAACTCTATTTATAGTTAGAAACTTGTCCTCGAGGTCTCTCTATAAACCTTTTTGTACGTCCATAAATGTGGAAATCTACCGATCTTTTTGTCTCCGTATATAGGGAAACAGCGTTTTCGCTATACCTGGGTACAAACAGAGTTTTGTAGCTCCACGTTTCGCTGTCTCGTTCCGTGGAGCCCTGGGGGTCCTTAGACATATACTCTTTTTACATAGTTGGATGGGGGTCTGTACCTAGTTAGCTCTAGCTCGAGACAGCGATAGAGAATTTTGTATACTTGTCCGTTTACGTGTACCCGGCGATCTGTCTATGTCTATGGATAGCCACGTTTATGTCGTTTTGTAGGTCGTTGTATATCGATATATAGAGCGCGGATAATTAGGTAGGTCGACCGCGCTGTGGCTCTATCTCTAGTTATTTGTAGGTCGATGTGTAGATGTAATTCTAGCTGGACATCCATACCTACCTGTGTTTGTAGGTATTTCCATAAAACCACAGCGATGTTTGTAGAAAACGCGCGCTACCCCTACACCGCTATATACATAATATATCTCTGTACAAAGATGTATAGAGATAAAGACACAGTTCGAAACCTATCGACTTGGACAAACAGTTGTTTATTTTTAAGTCGCTCGACCGAACTAGTTACACCGAGATCGATTTGTTTCTCTATACACCTCTCTCTGTGGAGAAACAGAGCGAGAAGTAGATTTCGAGAAGCCACCGGGACAATTACAGAAAGCGGTAGATTTACATACAAAGAAGGAGACTTATCGATACACATAGAGGTATCGATAACGATGTATACCTACATCCAGCTCCATACCTAAAGGTAGAAAGACATGTGTCGACATGTTTACGTTTAGATATGGACCTAGATATGTCTACGGACACGAGACTTACACGTCTAGATAGTTGTGTATTTCTCTCTGGACAGATCTGTAAAGGTACGTCTACATGTCGATATCGGTCTGTCGGTAGATAAAAATCTATATTTAGACCGATAACTAGGTCTCGATGTCGTTCTCTAACGATGGACCTGTAGACCGAAAAAGAACTTTTTGTTTTCCACAAGTCTAGACTTTTTTGGGTCTAGACACTTGTGGAATTCGAGATAGGGCTCTCCCTCTGGCTCTATAGATCGACGGGTATCGCTATCGAGACGTGGGTCGAGATGGGTATCTCGCTATACATGGATTTCCAACCTTGTAGGTGTCTCTCGAAGGCGGTAGGGACACAAAATAGCTGTAGCTACAACTACGTATCGATACATAAAGAGCTACAAATTGGGCAGCTGTCTATATGAATTATAAGTATACTTCTTTTTTTTACTTTGTTCAGAACAACTTCTCATTTTTTTCTACTCATAACTAGCATCACAAAATACGCAATAATAACGAGTAGTAACACTTTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAGTTTTCAATGTAAGAGATTTCGATTATCCACAAACTTTAAAACACAGGGACAAAATTCTTGATATGCTTTCAACCGCTGCGTTTTGGACCTATTCTTGACATGATATGACTACCATTTTGTTATTGTACGTGGGGCAGTTGACGTCTTATCATATGTCAAAGTCATTTGCGAAGCTTGGCAAGTTGCCAACTGACGAGATGCAGTAAAAAGAGATTGCCGTCTTGAAACTTTTTGTCCTTTTTTTTTTCCGGGGACTCTACGAACCCTTTGTCCTACTGATTAATTTTGTACTGAATTTGGACAATTCAGATTTTAGTAGACAAGCGCGAGGAGGAAAAGAAATGACAAAAATTCCGATGGACAAGAAGATAGGAAAAAAAAAAAGCTTTCACCGATTTCCTAGACCGGAAAAAAGTCGTATGACATCAGAATGAAATTTTCAAGTTAGACAAGGACAAAATCAGGACAAATTGTAAAGATATAATAAACTATTTGATTCAGCGCCAATTTGCCCTTTTCCATTCCATTAAATCTCTGTTCTCTCTTACTTATATGATGATTAGGTATCATCTGTATAAAACTCCTTTCTTAATTTCACTCTAAAGCATACCGCCAGGTACGTACGTATACAGAAATACATGTATCTGTGGATATCCGTACATCGAGCCACATATCCCTTTAACTGGCGAAATATACTTATACCGAAAATTAGAGGGAACGCGGTATATGTACGACCGACACAATGAAACTAGATTGCGTAATTTCTAGTGTAAACAAATATGGCTATCTAAATGTCTCTAGGTACATCGAAAGAAAGTTACATATATTTAAATCGATAACTACGTAGATGGGTTTCTAGTTGTAGAGCGACAAATCTCGAAAGCTCTTTTTGGAGAGGTAGATATATAGTATATATCGCTGTCGAAGTATACAAATATCTACTTCGATAACTAACCAACGGTATCGGTCTAGAAAAGTCTCGCCAGGTCCGTAAACAAAGAGGTACATAACGAGACCGGTGGGTGTTTCGGTATACACTTGTGGGTATCGAGACATGTATGTTTGTGTGTAACTATATCCAAGGTCTTTGTGGACTTGTAGAGGTGTATCTGTCGATATTTACGTC
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CSE 5290, Fall 2009

11. Importance of algorithms
– Compare human vs. mouse (blocks of 1,000 nucleotides)
• 3,000,000*3,000,000 comparisons, each 1,000*1,000 operations (w/dynamic progr.)
• At 1 trillion operations per second, it would take 104 days
– Search all regulatory motifs of length 20 (11^20) in the human genome
• 426 years
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CSE 5290, Fall 2009

12. Clustering flow cytometry data
1 million vectors
Each of length 25 (real numbers)
Need quick output!
Results should be biologically meaningful!
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CSE 5290, Fall 2009

13. R: introduction
Why R?
Lots of available libraries (statistics, machine learning,…..)
Very good visualization capability
Free
Multiplatform
Easy to publish code
Biologists use it!
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CSE 5290, Fall 2009

14. R - contd Grew out of a popular statistics package
Used extensively by statisticians and computational biologists
Lots of resources (see class web page)
Some similarities with MatLab
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CSE 5290, Fall 2009

15. R – strengths and weaknesses
Allows very quick testing of ideas
Libraries available for most purposes
Allows integration with C code
Weaknesses
Not as efficient as MatLab on matrix operations
Not very good at handling large data sets
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CSE 5290, Fall 2009

16. Next class Ch 3 of text In the meantime… Read Ch 1 and 2 on your own.
Get familiar with R
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CSE 5290, Fall 2009