Biological preliminaries
Answers
Introduction
References
Exercises
Analysis of individual sequences
Helical wheels, amphipatic helices and coiled-coils
Pairwise sequence comparison
Dot plots
Sequence Alignment
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
Suboptimal Alignments
Suboptimal points
Stability
Application
Variants of the dynamic programming algorithm
Free end-gaps
Local Alignments
Similarity and Distance
Parametric Alignments
Linear in Space Algorithm
Practical Sections on Pairwise Alignments
Alignment Applet
Alignment Quiz
Multiple sequence alignment
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
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
Different Levels of Protein Structure
Prediction Methods
Secondary Structure Prediction
Comparative Modelling
Related Links
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