Module Descriptors

Bioinformatics

MA215: Mathematical Molecular Biology (5 ECTS)

This course covers mathematical and algorithmic methods applied to problems in molecular biology, including genome sequence assembly, DNA and amino acid sequence alignment, phylogenetics and models of RNA secondary structure.

Taught in Semester(s) I. Examined in Semester(s) I.

Workload: 24 hours (24 Lecture hours).

Module Learning Outcomes. On successful completion of this module the learner should be able to:

  1. describe several problems in molecular sequence biology;
  2. use graph theoretical methods to solve toy genome assembly problems;
  3. apply algorithms to align homologous DNA sequences;
  4. infer phylogenetic trees using parsimony and/or genetic distance based methods;
  5. describe concepts in transformational grammars;
  6. determine the grammar class that corresponds to a set of rules;
  7. parse a DNA (or other) string using regular and context-free grammars;
  8. describe key concepts in systems biology.

Indicative Content

The module begins with a brief overview of some of the key concepts in molecular sequence biology, including DNA and DNA sequencing, the genetic code, the Central Dogma of molecular biology, genome biology, molecular evolution and phylogenetics. Some concepts in graph theory are introduced, followed by a demonstration of graph theoretical methods applied to the genome assembly problem, which consists of assembling collinear genome sequences from short, random fragments of the sequence that are generated in genome sequencing projects. The problem of aligning homologous (related by descent) sequences is introduced and solved using a dynamic programming algorithm. The course covers algorithms to infer evolutionary relationships (i.e. phylogenetic trees), using concepts such as evolutionary parsimony and genetic distance. Transformational grammars are introduced as well as their applications to the description of amino acid sequence motifs and the structure of RNA molecules. Depending on time, the course may include a review of concepts in systems biology and the analysis of biological networks.

Module Resources

  1. Biological Sequence Analysis
    Durbin, Eddy, Krogh & Mitchison
    Cambridge University Press

  2. Bioinformatics for Biologists
    Pevzner & Shamir (Eds.)
    Cambridge University Press

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