Online Lectures on Bioinformatics

Online Lectures on Bioinformatics

Biological preliminaries
Introduction
References
Exercises
Answers
Analysis of individual sequences
Introduction
Helical wheels, amphipatic helices and coiled-coils
References
Exercises
Pairwise sequence comparison
Introduction
Dot plots
Sequence Alignment
References
Exercises
Answers
Algorithms for the comparison of two sequences
Introduction: Type I and type II alignments
Type I alignment
Type II alignment
General gap functions for type II alignments
Minimum distance alignments
Minimum distance alignment score as a metric on sequences
References
Suboptimal Alignments
Introduction
Suboptimal points
Suboptimal Alignments
Stability
Application
References
Variants of the dynamic programming algorithm
Introduction
Free end-gaps
Local Alignments
Suboptimal Alignments
Similarity and Distance
Parametric Alignments
Linear in Space Algorithm
Practical Sections on Pairwise Alignments
Alignment Applet
Alignment Quiz
Multiple sequence alignment
Introduction
References
Exercises
Algorithms for SP-optimal multiple alignments
Definition
Motivation
Score functions
Problem
The exact solution
Saving space
Affine gap-costs
Reduction of search space
Divide-and-Conquer Alignment
References
Phylogenetic Trees and Multiple Alignments
Evolution
Ultrametric Trees
Iterative alignment strategy
Additive trees
Reconstruction of additive trees
Approximating additive metrics
Heuristics
Character-based methods for Phylogeny Construction
Parsimony
Protein Structure
Introduction
Different Levels of Protein Structure
Prediction Methods
Secondary Structure Prediction
Comparative Modelling
References
Related Links
Exercises
Links