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Genomics and Molecular Evolution

Objectives

Understand the basic mechanisms of molecular evolution. Understand how to search and retrieve sequence data from public databases. Know the basic aspects of Next Generation Sequencing technologies and the main steps involved in genome assembly and in genome analyses for population, comparative and functional genomics.

General characterization

Code

10717

Credits

3.0

Responsible teacher

Ana Rita Fialho Grosso, José Paulo Nunes de Sousa Sampaio

Hours

Weekly - 2

Total - 38

Teaching language

Português

Prerequisites

Basic knowledge of molecular genetics and evolution.

Bibliography

Vandamme, AM. 2009. Basic concepts of molecular evolution. In “The Phylogenetic Handbook”, Cambridge Univ Press

Descent with modification (Reading the story of DNA, L Bromham, 2008)

Teaching method

A limited number of lectures is scheduled. Autonomous study is encouraged. The recommended bibliography has to be studied in advance. Discussion sessions are included. Exercises will be carried out in practical sessions using personal computers and a dedicated server.

Evaluation method

The avaliation consists in one individual test and a group project, contributing respectively for 60% and 40% of the final grade. For approval a minimal final grade of 10 (on a 0 to 20 system) has to be obtained.

The test is individual, without consulting and performed during 45 min. For final approval a minimal test grade of 9,5 has to be obtained.

The group project consists in the integration of data and information in order to produce new knowledge, which contents should be present in a report.

Subject matter

Topic 1

  • Biological and Molecular Evolution.
  • Basic concepts about treatment and sequence search.

 Topic 2

  • Genome Evolution: detection of horizontal transfer.
  • Construction of molecular phylogenies.

Topic 3

  • Molecular and Functional Genomics: genes, gene expression and function.
  • Gene characterization: genes, genomics coordinates, transcripts, proteins, comparatica genomics, genetic variants.

Topic 4

  • Molecular and Functional Genomics: high-throughput sequencing technologies.
  • Search and interpretation of transcriptome data.

Topic 5

  • Genomics in Biomedicine
  • Genomics in cancer: mutations, chromsomal alterations, transcripts, proteins, clinic impact.

Topic 6

  • Genomics: data, information, knowledge.
  • Basic concepts for data integration, gathering information and results presentation.