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Algorithms for Computational Biology

Lecture Notes

Below is a partial selection of lecture notes that approximate chronologically the topics and themes listed on thecalendar. The lecture notes are under development.

LEC #

TOPICS

1

Computational Challenges (PDF)

2

BLAST (PDF)

3

Motif Discovery (PDF - 1.2 MB)

4

Gibbs Sampling (PDF)

5

Sequence Alignment (PDF - 1.4 MB)

6

RNA Secondary Structure

7

HMMs and Gene Finding (PDF)

8

Genome Evolution and Phylogenetic Trees

9

Phylogenetic Trees

10-11

Genome Rearrangements, Genome Duplication

12

Biological Networks

Assignments

A programming component was included in several of the problem sets. For those problem sets, data sets were given and the students were asked to implement their algorithms using python. To learn more about python, you can visit their Web site.

Problem Set 1 (PDF)

Problem Set 2 (PDF)

Problem Set 3 (PDF)

  • viterbi.py (PY)
  • cpgislands (TXT)
  • cluster.py (PY)
  • tools.py (PY)
  • clustalw (TXT)

Problem Set 4 (PDF)