Calendar · Lecture Notes
MIT OpenCourseWare
Introduction to Computational Molecular Biology
- Instructor
- Ross Lippert
- Term
- Fall 2004
- Level
- Graduate
- What's inside
- 1 lecture note · 1 reading · 24 other files · 5 web pages
- Materials open
- MIT OCW
About this course
Source: MIT OpenCourseWare 18.417 Introduction to Computational Molecular Biology, Fall 2004, Ross Lippert — original course page on ocw.mit.edu ↗. License: CC BY-NC-SA 4.0. Study order: MIT's own listing order, section by section. Taken from MIT's published course files, downloaded from ocw.mit.edu on September 23, 2026. How RedLectern is built.
Materials are grouped the way MIT organized them. A verified, course-wide order has not been established here.
Before you start
Prerequisites are not listed here. Check MIT's own syllabus for this course.
How this course was organized
What's here, and what isn't
- MIT's own materials here did not support a verified, course-wide order, so they are grouped by section instead.
Not included here
17 items from the source could not be safely included:
- MIT's page format for this item wasn't recognized clearly enough to place it safely. (17 items)
Materials by section
Grouped by section, as MIT organized them. Not sequenced or ordered.
Lecture Notes
15 files
- Motifs and Median Strings (Courtesy of Jerome Mettetal. Used with permission.) A Review Paper on Regulatory Motifs Download
- Global Alignment (Courtesy of Russ Cox and Michael Walfish. Used with permission.) Download
- Local Alignment (Courtesy of Anthony W. Scelfo and Athicha Muthitacharoen. Used with permission.) Download
- Spliced Alignment (Courtesy of Lele Yu and Sam Kaufman. Used with permission.) Download
- More Efficient Alignment (Courtesy of Mark Halsey and Robert Edward Beverly. Used with permission.) Download
- Peptide Graphs (Courtesy of Robert Edward Beverly and Christopher J. Peikert. Used with permission.) Download
- Exact Pattern Matching (Courtesy of Lele Yu and Mark Halsey. Used with permission.) Download
- Suffix Trees (Courtesy of Athicha Muthitacharoen and Anthony W. Scelfo. Used with permission.) Download
- Suffix Arrays and BWTs (Courtesy of Tushara C. Karunaratna and Peter Wai Kei Lee. Used with permission.) Download
- BLAST (Courtesy of Eitan Reich and Peter Lee. Used with permission.) Download
- Trees (Courtesy of Eugenia Lyashenko. Used with permission.) Download
- Hidden Markov Models I (Courtesy of Han-Pang Chiu and Russ Cox. Used with permission.) Download
- Hidden Markov Models II (Courtesy of Chris Peikert. Used with permission.) Download
- Gibbs Sampling (Courtesy of Tushara C. Karunaratna. Used with permission.) Download
- Random Projections (Courtesy of Eugenia Lyashenko. Used with permission.) Download
Assignments
- Problem Set 1 Download
- Problem Set 2 Download
- Problem Set 3 Download
- Problem Set 4 Download
- Problem Set 5 Download
- Problem Set 6 Download
Projects
- Burrows-Wheeler Transforms in Linear Time and Linear Bits (Courtesy of Russ Cox. Used with permission.) Download
- Sampling Good Motifs with Markov Chains (Courtesy of Christopher J. Peikert. Used with permission.) Download
- Robust Clustering Techniques in Bioinformatic (Courtesy of Robert Edward Beverly. Used with permission.) Download
Course outline
Calendar · Lecture Notes
Lecture 2: Partial Digest Problem
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Lecture 3: Motifs and Median Strings
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Lecture 4: Global Alignment
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Lecture 5: Local Alignment
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Lecture 6: Spliced Alignment
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Lecture 7: More Efficient Alignment
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Lecture 8: Genomics and SBH Graphs
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Lecture 9: Peptide Graphs
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Lecture 10: Exact Pattern Matching
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Lecture 11: Suffix Trees
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Lecture 12: Suffix Arrays and BWTs
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Lecture 13: BLAST
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Lecture 14: Clustering (Guest Lecturer)
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Lecture 15: Trees
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Lecture 16: Review of Phylogenetic Analysis Coalescent Theory in Biology
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Lecture 17: Application: Microarrays (Guest Lecturer)
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Lecture 18: Hidden Markov Models I
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Lecture 19: Hidden Markov Models II
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Lecture 20: Gibbs Sampling
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Lecture 21: Random Projections
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Lecture 22: MCMC and Bayesian Networks
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Lecture 23: The Future: Protein Structure (Guest Lecturer)
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Lecture 24: The Future: Haplotype Mapping (Guest Lecturer)
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Lecture 25: Presentations of Final Projects
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Lecture 26: Presentations of Final Projects (cont.)
MIT OpenCourseWare, Ross Lippert, 18.417 Introduction to Computational Molecular Biology, Fall 2004.
License: CC BY-NC-SA 4.0 · Edition: Fall 2004 · Open the original course on OCW ↗
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