Bioinformatics - Michaelmas 2012

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

News

     

Content

Basic 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: the Burrows-Wheeler transform
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

Lectures

     Lecture notes Slides
        1 slides/page colour PDF
       Examples
 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