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Functional genomics and bioinformatics

Code:

MEBQB12

Sigla:

GFB

Áreas Científicas
Classificação	Área Científica
OFICIAL	Biotecnologia

Ocorrência: 2023/2024 - 1S

Ativa?	Yes
Unidade Responsável:	Departamento de Engenharia Química e Biológica
Curso/CE Responsável:	Master in Biological and Chemical Engineering

Ciclos de Estudo/Cursos

Sigla	Nº de Estudantes	Plano de Estudos	Anos Curriculares	Créditos UCN	Créditos ECTS	Horas de Contacto	Horas Totais
MEBQ	1	Study Plan	2	-	5	45	135

Língua de trabalho

Portuguese

Objetivos

This curricular unit is designed primarily to provide students with an integrated view of the structure and function of genes and genomes, taking into account advances in methods of sequencing, annotation and analysis. Students are expected to use bioinformatics tools to perform sequence searches and analysis and comprehend their usefulness for function prediction as well as acquiring knowledge about the analysis of RNA and protein expression.

Resultados de aprendizagem e competências

Não Aplicável

Modo de trabalho

Presencial

Pré-requisitos (conhecimentos prévios) e co-requisitos (conhecimentos simultâneos)

Não Aplicável

Programa

1-Organizational structure of genomes; Methods for genome sequencing, genome analysis and annotation.
2-Evolution of genomes and molecular phylogeny. Comparative Genomics. Definition of orthologs and paralogs genes.
3-Analysis of the genome-wide gene expression by proteomics and transcriptomics approach.
4-Functional Genomics. Metabolomics, RNomics, metagenomics and other omics.
5-Applications of bioinformatics in genomics. Algorithms for sequence alignment: single and multiple alignments; motif-search algorithms: motif representation and search systems available on the web
6-Biotechnological applications.

Laboratorial practical classes:
Use of bioinformatic tools to perform sequence alignments and sequence database searches (BLAST e Clustal), phylogenetic analysis and cladograms, motif search and prediction of gene function, prediction of protein structure, interpretation of biological significance of genome-scale data.

Bibliografia Obrigatória

C.W. Sensen; Handbook of Genome Research, vol Handbook of Genome Research, vol. I e vol. II , 2005. ISBN:  ISBN 3-527-31348-6
T. A. Brown. Gee; Cloning and DNA Analysis, An Introduction, Blackwell Publishing, 2006
Terry Brown; Genomes, Bios Scientific Publishers Oxford, 2006. ISBN: ISBN 9780815341383
Robert F. Weaver; Molecular Biology, McGraw Hill, 2005. ISBN: ISBN: 007-124344-5
A.D. Baxevanis, B.F.F. Ouellette; Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Wiley Interscience, 2005. ISBN: ISBN 978-0-471-38391-8
M. Borodovsky, S. Ekisheva; Problems and Solutions in Biological Sequence Analysis, Cambridge University Press, 2007. ISBN: ISBN 978-0-521-61230-2
Mount, D; Bioinformatics: Sequence and Genome Analysis, 2.ª edição, Cold Spring Harbor Laboratory Press, 2004. ISBN: ISBN 978-0-879-69712-9
Durbin, R., Eddy, S.R., Krogh, A., Mitchison, G; Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Cambridge University Press, 2004. ISBN: ISBN 978-0-521-62971-3

Métodos de ensino e atividades de aprendizagem

The curricular unit (UC) is taught using expository and demonstrative methods with computerized support of Powerpoint. The UC consists of a theoretical-practical component, in which students will discuss current topics in the field of structural, evolutionary and functional genomics and new omics technologies. The laboratory practical component aims to familiarize students with the tools and databases available, and to apply the theoretical contents in the bioinformatics analysis applied to several case studies.

Continuous Assessment:
50% x Test +40% x written Work + 10% Class Assessment

Assessment 1st / 2nd season and special season:
100% xExame (minimum score in the exam of 9.5) OR 60% x Exam +40% x written Work

Tipo de avaliação

Distributed evaluation with final exam

Componentes de Avaliação

Designation	Peso (%)
Teste	50,00
Trabalho escrito	40,00
Participação presencial	10,00
Total:	100,00

Componentes de Ocupação

Designation	Tempo (Horas)
Estudo autónomo	80,00
Frequência das aulas	42,00
Trabalho de investigação	0,00
Trabalho escrito	10,00
Trabalho laboratorial	3,00
Total:	135,00

Obtenção de frequência

not applicable

Fórmula de cálculo da classificação final

Continuous Assessment: 50% x 1st Test + 40% Work + 10% Class Assessment 

1st / 2nd season evaluation and special season: 100% x Exam (9,5 out of 20 to get approval) OR 60% x Exam +40% x written Work

Observações

- As part of the continuous assessment, a class will be held in a computer laboratory in order to perform a task based on access to an online database called PATRIC - Pathosystems Resource Integration Center. Students will have to use the genome of bacteria (pathogenic or not) to create a comparative analysis between the different genomes of a species. However, this analysis will consider the protein content of the genome, thus having the functional genome. Gene content analysis will be explored in order to explain issues associated with biochemical pathways and participation in infectious processes (pathogen cases) or biotechnological (non-pathogenic cases).

 

- The group work referred in the evaluation consists on the analysis of a scientific article (assigned by the teacher) and its presentation with the aid of a Powerpoint file, with a maximum duration of 30 minutes. The presentation will be the subject of a dynamic discussion, with a short question and answer period.