Online Lectures on Bioinformatics

# Biological preliminaries

* Introduction

* References

* Exercises

o 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

o 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

via Online Lectures on Bioinformatics.

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