Bioinformatics - Michaelmas 2013

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

News

     

Content

    Introduction to biological data: Bioinformatics as an interesting field in computer science.

    Dynamic programming. Longest common subsequence, DNA, RNA, protein structure alignment, linear space alignment, heuristics for multiple alignment.

    Sequence database search. Blast, Patternhunter.

    Next Generation Sequencing. De Bruijn graph, Burrows–Wheeler transform.

    Phylogeny - parsimony-based. Fitch, Wagner, Sankoff parsimony.

    Phylogeny - distance-based. UPGMA, Neighbour Joining.

    Clustering. K-means, Markov Clustering algorithm.

    Applications of Hidden Markov Models.

    Searching motifs in sequence alignment. Gibbs sampling.

    Biological networks: reverse engineering algorithms and dynamics; Wagner, Gillespie.

   Example Questions and answers

Lectures

     Lecture notes Slides
        1 slides/page colour PDF

Supplementary figures 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