Comparative Genomics

24 outubro 2013, 09:30 • Arsénio do Carmo Sales Mendes Fialho

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

Genomic Tools

24 outubro 2013, 08:00 • Arsénio do Carmo Sales Mendes Fialho

NCBI Genome Database

Genome sequence projects

Gene plot (similarities among bacterial genomes)

MAGE Genome Browser interface

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

Comparative Genomics

23 outubro 2013, 12:30 • Arsénio do Carmo Sales Mendes Fialho

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

Genomics Tools

23 outubro 2013, 11:00 • Arsénio do Carmo Sales Mendes Fialho

NCBI Genome Database

Genome sequence projects

Gene plot (similarities among bacterial genomes)

MAGE Genome Browser interface

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

Evolutionary inference using phylogenetic trees and comparative genomics

18 outubro 2013, 11:00 • Miguel Nobre Parreira Cacho Teixeira

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.

Methods of construction of phylogenetic trees. Distance methods: least squares (LS) and clustering approaches (UPGMA). Maximum likelihood.

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.

This class was taught by Dr. Paulo Jorge Dias, a post-doctoral researcher at the BSRG