Bioinformatics II: Algorithms and Data Analysis

Draft lecture timetable for 2003/04 based on 2002/2003 delivery

Lecture 1 Introduction
Introdcution to Bioinformatics; Introduction to Sequence Alignment; Substitution Matrices; Gap Penalties.

Lecture 2 Pair-wise Sequence Alignment
Global Alignment; Local Alignment; Ends-free Alignment; Dynamic Programming; Complexity; Divide and Conquer; Gap Penalty Algorithms; Introduction to Heuristics.

Lecture 3 Heuristics and Biological Databases.
FASTA; BLAST; EMBL; Genbank; DDBJ; PDB; Pfam; InterPro.

Lecture 4 Guest Lecture on Alignment Methods: Dr Shane Sturrock, Aneda Ltd

Lecture 5 Multiple Sequence Alignment; Protein Families.
CAP (Contig Assembly Program) http://bioweb.pasteur.fr/seqanal/interfaces/cap.html
ClustalW http://www.ebi.ac.uk/clustalw/

Lecture 6 Gene Finding, Functional Genomics and Proteomics.

Lecture 7 Systems Biology and Networks. Using Bayesian Networks to analyse Gene Expression Data
Bayesian Networks without Tears
The large-scale organisation of metabolic networks

Lecture 8 Guest Lecture on Phylogenetics: Dirk Husmeier, BIOSS

Lecture 9 Guest Lecture on BioJava: Matthew Pocock.

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