Bioinformatics


News

1 Example class  (to be decided between 17 April, 17 May 2013)   

Content of the Lecture Notes

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 : 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

Lectures

     Lecture notes Slides
        1 slides/page colour (see note below)
 PDF
       1 Example - slides/page colour PDF

Errata
 PDF



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).

Reading

Jones, Pevzner Introduction to Bioinformatics algorithms, MIT Press

Joe Felsenstein Phylogeny Elsevier

Biological Sequence Analysis: Probabilistic Models of Proteins and
Nucleic Acids
 Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison
 http://books.google.co.uk/books/about/Biological_Sequence_Analysis.html?id=R5P2GlJvigQC

Tutorials for Molecular Biology (accessible to computer science
students) http://www.thomas-schlitt.net/Bioproject.html;
http://www.biostat.wisc.edu/ craven/hunter.pdf

Software Resources

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