Evolutionary inference using phylogenetic trees and comparative genomics

22 outubro 2014, 12:30 • Paulo Jorge Moura Pinto da Costa Dias

Introduction to the proposed problem on the reconstruction of the evolutionary history of ATR1 gene and ORF YMR279C.

Multiple alignment of the 37 amino acid sequences (using MUSCLE software). Analysis of the sequence aligment using JALVIEW and interpretation of results.

Construction of the phylogenetic tree using the tools made available by the Institute Pasteur Portal MOBYLE bioinformatics portal. Distance methods (PROTDIST and NEIGHBOR algorithms).  Maximum parsimony method (PROTPARS algorithm). Maximum likelihood method (PHYML algorithm). Comparison of the phylogenetic trees obtained using DENDROSCOPE software.

Introduction to network visualizing software Cytoscape. Basic operations in the software, including creation of sub-networks, etc. Network based neighbourhood analysis of the evolutionary history of ATR1 gene and ORF YMR279C.

Discussion about the sequence similarity and gene neighbourhood methodologies.

Introduction to key evolutionary concepts, to phylogenetic trees and to phylogenomics

22 outubro 2014, 11:00 • Paulo Jorge Moura Pinto da Costa Dias

Basic concepts of the theory of evolution. Evolution versus Creationism. Three different concepts of evolution. Basic concepts of population genetics. The synthesis of the theory of evolution. Gradualism versus punctuated equilibrium. The importance of fossil record. Macroevolution and extrapolationism. Species Concept. Modes of speciation.Mechanisms of reproductive isolation. Three schools of macrotaxonomy. Concepts of monophyly, paraphyly and polyphyly.

Introduction to phylogenetic trees. Cladograms, additive trees and ultrametric trees. Metric and additive distances. Ultrametric distances. Rooted and unrooted trees. Methods of rooting the phylogenetic tree: outgroup and molecular clock methods. How many rooted and unrroted trees are there? Empirical tree construction. Methods of tree construction. Methods of construction of phylogenetic trees. Maximum parsimony. Distance methods: least squares (LS) and clustering using Unweighted Pair Group Method with Arithmetic Mean (UPGMA) algorithm.

Concepts of homology and homoplasy of features. Parallel and convergent evolution and secondary loss of a feature. Homology among genes. Orthologs and paralogs genes. Gene trees and species trees.

Phylogenomics. Gene content and gene order methods. Phylogenomic networks.

Comparative Genomics

17 outubro 2014, 11:00 • Arsénio do Carmo Sales Mendes Fialho

Comparative Genomics - MAGE - Microbial Genome Annotation System; MAGE basic functionalities; synteny maps

Comparative Genomics

16 outubro 2014, 09:30 • Arsénio do Carmo Sales Mendes Fialho

 Comparative Genomics - MAGE - Microbial Genome Annotation System; MAGE basic functionalities; synteny maps

Genomic Tools

16 outubro 2014, 08:00 • Arsénio do Carmo Sales Mendes Fialho

 NCBI Genome Database

 Genome sequence projects

 Gene plot (similarities among bacterial genomes)

 STRING(search tool for the retrieval of interacting genes/proteins)