Bioinformatics - Michaelmas 2011

Lecturer: Dr P. Lio'
Lecture Theatre 2, WGB

News

     

Content

  Key concepts in genetics.
  Dynamic programming (Longest Common Subsequence,
  DNA, RNA alignment, linear space alignment).
  Progressive alignment
  Homology database search (Blast, Patternhunter).
  Phylogeny - parsimony-based - (Fitch, Wagner, Sankoff).
  Phylogeny - distance based - (UPGMA,Neighbour Joining).
  Phylogeny (consensus tree, tree rearrangements algorithms)
  Clustering (K-means, Markov Clustering algorithm)
  Hidden Markov Models applications in Bioinformatics (Viterbi,
Forward-Backward, Baum-Welch).
 Pattern search (Gibbs sampling)
 Biological Networks reconstruction (Wagner).
 Simulation of Biological Networks (Gillespie).

Lectures

     Lecture notes Slides
        4 slides/page colour PDF
      
































Reading

Jones, Pevzner Introduction to Bioinformatics algorithms, MIT Press

Material/links

General: National Center for Biotechnology Information  http://www.ncbi.nlm.nih.gov/
Human Genome Browser Gateway http://genome.ucsc.edu/
Ensembl Genome Browser  www.ensembl.org;
EBI  http://www.ebi.ac.uk;
http://www.expasy.ch/sprot/; http://www.genome.jp/kegg/; http://www.rcsb.org/pdb;
http://www.bioinformatics.ca/
Alignment:
 www.clustal.org; http://www.drive5.com/muscle/;
Trees: http://evolution.genetics.washington.edu/phylip.html
Programming:  Matlab: http://www.mathworks.com/products/bioinfo/
BioJava - www.biojava.org;  BioPerl - www.bioperl.org; BioPython - www.biopython.org;
BioCorba -www.biocorba.org; C++ www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC;
http://cran.r-project.org/; http://sbml.org/Main_Page
Past exam papers