Calendar · Lecture Notes
MIT OpenCourseWare
Algorithms for Computational Biology
Art: not stated, Fletcher's Combined Block Telegraph Apparatus and Bell, 1889 · Public domain
- Instructor
- Prof. Manolis Kellis
- Term
- Spring 2005
- Level
- Undergraduate
- What's inside
- 1 lecture note · 30 other files · 3 web pages
- Materials open
- MIT OCW
About this course
Source: MIT OpenCourseWare 6.096 Algorithms for Computational Biology, Spring 2005, Prof. Manolis Kellis — 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
- A lecture sequence of 12 items is confirmed. It stays as organized materials rather than a full course order.
Not included here
2 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. (2 items)
Materials by section
Grouped by section, as MIT organized them. Not sequenced or ordered.
Lecture Notes
- Computational Challenges Download
- BLAST Download
- Motif Discovery Download
- Gibbs Sampling Download
- Sequence Alignment Download
- HMMs and Gene Finding Download
Assignments
17 files
- Problem Set 1 Download
- intergenic Download
- conserved Download
- code template Download
- Problem Set 2 Download
- code Download
- ACE2 Download
- MBP1 Download
- DIG1 Download
- relevant code Download
- Problem Set 3 Download
- This is a supporting file for the programming component of the problem set 3 (viterbi.py) Download
- cpgislands Download
- This is a supporting file for the programming component of the problem set 3 (cluster.py) Download
- This is a supporting file for the programming component of the problem set 3 (tools.py) Download
- clustalw Download
- Problem Set 4 Download
Other materials from this course
7 files
- This file explains setup, the BLAST algorithm, BLAST extensions, substitutions matrices, K-mers… (lecture2.pdf) Download
- This file explains comparing genomes, comparing two DNA sequences, re-use computation, memoization… (lecture5.pdf) Download
- This file explains the world before DNA or protein, RNA world, RNA invented its successors, most… (lecture6.pdf) Download
- This file explains early evolution, the last 3.5 billion years, phylogenetic trees, UPGMA, neighbor… (lecture9.pdf) Download
- This file explains genome correspondence, chromosome evolution, genome rearrangements, sorting by… (lecture10and11.pdf) Download
- This file explains microarray technology, clustering gene expression, TF binding, Bayesian… (lecture12.pdf) Download
- This file explains computational model (simple Markov models, hidden Markov models), working with… (lectures7and8.pdf) Download
Course outline
Calendar · Lecture Notes
Lecture 2: Rapid Database Search (Hashing)
Calendar · Lecture Notes
Lecture 3: Regulatory Motif Discovery (Combinatorial Search)
Calendar · Lecture Notes
Lecture 4: Probabilistic Motif Finding (Gibbs Sampling)
Calendar · Lecture Notes
Lecture 5: Sequence Alignment (Dynamic Programming)
Calendar · Lecture Notes
Lecture 6: Markov Chains and Hidden Markov Models
Calendar · Lecture Notes
Lecture 7: Gene Finding
Calendar · Lecture Notes
Lecture 8: Genome Evolution and Phylogenetic Trees
Calendar · Lecture Notes
Lecture 9: Genome Duplication
Calendar · Lecture Notes
Lecture 10: Gene Expression Clustering
Calendar · Lecture Notes
Lecture 13: Scale-free Networks
Calendar · Lecture Notes
Lecture 14: Comparative Genomics
MIT OpenCourseWare, Prof. Manolis Kellis, 6.096 Algorithms for Computational Biology, Spring 2005.
License: CC BY-NC-SA 4.0 · Edition: Spring 2005 · Open the original course on OCW ↗
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