Computational Biology

This is the page where I keep material related to my computational molecular biology lectures. You probably got here from the COMP4900/5108 webpage.

More Dynamic Programming Algorithms (Feb. 8)

Tweaks on Sequence Alignment

• Reducing from quadratic to linear space (Section 7.2)
• The four-russians speedup (Sections 7.3 & 7.4)

Minimum Parsimony

• Sankoff's and Fitch's algorithms (Section 10.10)

RNA Secondary Structure Predication

• Evangelos' slides (relevant material starts on page 25)

Lecture on Dynamic Programming Algorithms (Jan. 25)

Sequence Alignment

• Most material is from Chapter 6 of the textbook
• My (handwritten and scanned) lecture notes

Lecture on Brute-Force Algorithms (Jan. 11)

Restriction Mapping

• Steven S. Skiena and Gopalkrishnan Sundaram. A Partial Digest Approach to Restriction Site Mapping, Bulletin of Mathematical Biology, 56, pages 275-294, 1994.
• Steven S. Skiena, Warren D. Smith, and Paul Lemke. Reconstructing sets from interpoint distances. Symposium on Computational Geometry pages 332-339, 1990 [ps]
• Pictures of Gel Electrophoresis
• Pseudocode for partial digest algorithm

Motif Finding

• Wyeth W. Wasserman and William Krivan, In silico identification of metazoan transcriptional regulatory regions. Naturwissenschaften 90(4):156-66. (2003). [pdf]
• Software: ALSE, Concensus, MITRA, Gibbs Sampler, and MEME

Resolving Conflicts in Multiple-Sequence Alignments

• Notes on Vertex-Cover Algorithms
• Ulrike Stege. Resolving conflicts in problems from computational biology.
  Doctoral Dissertation 13364, ETH Zürich, Institute of Scientific Computing, 2000. [pdf]
  (See discussion beginning on page 91.)