Online Lectures on Bioinformatics
Online Lectures on Bioinformatics
- Biological preliminaries
- Analysis of individual sequences
- Pairwise sequence comparison
- 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
- 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 statistics
- Introduction
- The Karlin-Altschul formula
- Statistical Significance of Local Smith-Waterman-Alignments
- References
- Exercises
- 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
- 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
- Database searching
- Physical Mapping and Sequence Assembly
- Protein Structure
- Introduction
- Different Levels of Protein Structure
- Prediction Methods
- Secondary Structure Prediction
- Comparative Modelling
- References
- Related Links
- Exercises
- Links
Comments are very welcome.
luz@molgen.mpg.de