News1 Example class (to be decided between 17 April, 17 May 2013)
Content of the Lecture NotesBasic concepts in Genetics and Genomics.
Dynamic programming (Longest Common Subsequence, DNA, RNA alignment, linear space alignment).
Progressive alignment (Clustal).
Alignment of Short reads to a reference genome : advantage of the Burrows-Wheeler transform for compressing data
Homology database search (Blast, Patternhunter).
Phylogeny - parsimony-based - (Fitch, Wagner, Sankoff).
Phylogeny - distance based - (UPGMA,Neighbour Joining).
Phylogeny (consensus tree, tree rearrangements).
Clustering (K-means, Markov Clustering)
Hidden Markov Models applications in Bioinformatics (Genescan, TMHMM).
Pattern search in sequences (Gibbs sampling).
Biological Networks reconstruction (Wagner) and simulation (Gillespie).
Example Questions and answers
Nota Bene: Some of the images shown in these lectures come from several
sources that have welcomed instructors to use them for educational
purposes (Felsenstein, Moran, Gerstein, Yang, Arkin, Leibler,
Batzoglou, Pevzner, Nussinov).
||1 slides/page colour (see note below)
||1 Example - slides/page colour
Jones, Pevzner Introduction to Bioinformatics algorithms, MIT Press
Joe Felsenstein Phylogeny Elsevier
Biological Sequence Analysis: Probabilistic Models of Proteins and
Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison
Tutorials for Molecular Biology (accessible to computer science
Past exam papers
Programming: Matlab: http://www.mathworks.com/products/bioinfo/