Introduction to Computational Biology Lecture # 18: Evolution - Parsimony

Assessing the Accuracy of Ancestral Protein Reconstruction Methods

The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of the reconstruction method. Every inference method leads to errors in the ancestral protein sequence, resulting in potentially misleading estimates of the ancestral protein's properties. To assess t...

Graph Theoretical Insights into Evolution of Multidomain Proteins

We study properties of multidomain proteins from a graph theoretical perspective. In particular, we demonstrate connections between properties of the domain overlap graph and certain variants of Dollo parsimony models. We apply our graph theoretical results to address several interrelated questions: do proteins acquire new domains infrequently, or often enough that the same combinations of doma...

Introduction to Computational Biology Lecture # 14: MCMC - Markov Chain Monte Carlo

Reconstructing Ancestral Genomic Sequences by Co-Evolution: Formal Definitions, Computational Issues, and Biological Examples

The inference of ancestral genomes is a fundamental problem in molecular evolution. Due to the statistical nature of this problem, the most likely or the most parsimonious ancestral genomes usually include considerable error rates. In general, these errors cannot be abolished by utilizing more exhaustive computational approaches, by using longer genomic sequences, or by analyzing more taxa. In ...

Introduction to Computational Biology Lecture # 17: RNA Structure from Sequence

In the previous lesson we presented a Stochastic Context Free Grammar model for prediction of RNA secondary structure from sequence. This model enables us to assign a probabily for every possible folding of a given RNA sequence. We will start this lecture with some comments about the relation between probabilities and energies. Then we will learn how to calculate the probabilities of structural...