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Ph.D. course in Biological Sequence Analysis

April 19 - 30, 2004

Sequence Analysis   Structure Prediction   Biological Function

A two week Ph.D. course will be held from April 19 - 30, 2004 covering biological macromolecules from sequence analysis through 3D-structure to the understanding of biological function at the molecular level.

The course will be relevant for Ph.D. students within biochemistry, physics, chemistry or molecular biology with an interest in DNA, RNA and/or proteins. The following topics will be covered:

  • Nucleotide and amino acid sequences: advanced multiple alignment methods, sequencing, database overview, gene finding, phylogeny reconstruction.

  • Protein, RNA and DNA structure: prediction tools, artificial neural networks, genetic algorithms, hidden Markov models, threading, structural alignment, homology modelling, protein surface and secondary structure prediction, DNA bending, RNA secondary structure.

  • DNA microarrays: Analysis of DNA microarray data including normalization, significance, clustering, principal component analysis, reverse engineering of regulatory networks and promoter analysis.

  • Protein and gene function: protein dynamics, catalytic mechanisms, binding sites and binding energies, docking, energy minimization, structure based drug design, gene function prediction
The course will consist of lectures and computer exercises, where the students will be introduced to a range of computational methods used in the field and to Internet biocomputing services available. It is arranged by Center for Biological Sequence Analysis at BioCentrum-DTU.

Teachers will include: Søren Brunak Steen KnudsenDave Ussery Anders G. PedersenNikolaj Blom
and some guest lecturers


The book: A Biologist's Guide to Analysis of DNA Microarray Data. by S. Knudsen (2002) will be available at the DTU bookstore (building 101A).

For more information, contact Anders Gorm Pedersen or Johanne Keiding, or see: