CS 262 Computational Genomics Spring 2003 (Old Handouts)

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Homeworks and Logistics

• Course Information (HTML)
• Course Syllabus (HTML)
• Course Staff (HTML)
• Problem Set #1 (PS) (PDF)
• Problem Set #2 (PS) (PDF)
• Problem Set #3 (PS) (PDF)
• Problem Set #4 (PS) (PDF)
• Final #1 (PS) (PDF).
• Final #2 (PS) (PDF).

This year's lecture notes

• Lecture 1, 4/01. Slides: (PPT), (PDF). Notes: (PS), (PDF).
• Lecture 2, 4/03. Slides: (PPT), (PDF). Notes: (PDF).
• Lecture 3, 4/08. Slides: (PPT), (PDF). Notes: (PDF).
• Lecture 4, 4/10. Slides: (PPT), (PDF). Notes: (DOC), (PDF).
• Lecture 5, 4/15. Slides: (PPT), (PDF). Notes: (DOC), (PDF).
• Lecture 6, 4/17. Slides: (PPT), (PDF)
• Lecture 7, 4/22. Slides: (PPT), (PDF). Notes: (DOC), (PDF).
• Lecture 8, 4/24. Slides: (PPT), (PDF). Notes: (DOC), (PDF).
• Lecture 9, 4/29. Slides: (PPT), (PDF)
• Lecture 10, 5/01. Slides: (PPT), (PDF). Notes: (PDF).
• Lecture 11, 5/08. Slides: (PPT), (PDF). Notes: (DOC), (PDF).
• Lecture 12, 5/13. Slides: (PPT), (PDF). Notes: (PDF).
• Lecture 13, 5/15. Slides: (PPT), (PDF). Notes: (DOC), (PDF).
• Lecture 14, 5/20. Slides: (PPT), (PDF). Notes: (DOC), (PDF).
• Lecture 15, 5/22. Slides: (PPT), (PDF). Notes: (DOC), (PDF).
• Lecture 16, 5/27. Slides: (PPT), (PDF). Notes: (DOC), (PDF).
• Lecture 17, 5/29. Slides: (PPT), (PDF). Notes: (DOC), (PDF).
• Lecture 18, 6/03. Slides: (PPT), (PDF). Notes: (DOC), (PDF).

Last year's lecture notes

• Lecture 1 (PDF)
• Lecture 2 (PDF)
• Lecture 3 (PDF)
• Lecture 4 (PDF)
• Lecture 5 (PDF)
• Lecture 6 (PDF)
• Lecture 7 (PDF)
• Lecture 8 (PDF)
• Lecture 9 (PDF)
• Lecture 10 (PDF)
• Lecture 11 (PDF)
• Lecture 14 (PDF)
• Lecture 15 (PDF)
• Lecture 16 (PDF)

Papers and Other Reference Materials

• Genscan: Prediction of Complete Gene Structures in Human Genomic DNA (PDF)
• Transcriptional Regulation of the Stem Cell Leukemia Gene (PDF)
• T-Coffee: A Novel Method for Fast and Accurate Multiple Sequence Alignment (PDF)
• LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA (PDF)
• Glocal Alignment: Finding Rearrangements During Alignment (PDF)
• AVID: A Global Alignment Program (PDF)
• BLAT: The BLAST-Like Local Alignment Tool (PDF)
• Gapped BLAST and PHI-BLAST (PDF)
• Pattern Hunter: Faster and more sensitive homology search (PDF)
• The estimation of statistical parameters for local alignment score distributions (PDF)
• ARACHNE 2: Whole-genome sequence assembly for Mammalian Genomes (PDF)
• The Eulerian path approach to DNA fragment assembly (PDF)

• A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition (PDF)
• ARACHNE: A Whole-Genome Shotgun Assembler (PDF)
• Genome Sizes (HTML)
• Transposons (HTML)
• Prediction of Complete Gene Structures in Human Genomic DNA (PDF)
• SLAM - Cross-species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model (PDF)
• Integrating Genomic Homology into Gene Structure Prediction (PDF)
• Christopher Burge's PhD Thesis (PS) (PDF)
• Identifying DNA and Protein Patterns with Statistically Significant Alignments of Multiple Sequences (PDF)
• Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment (PDF)

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