Biocomputing

Code: BIO12359L

6 ECTS

Duration: 15 weeks/156 hours

Scientific Area: Biological Sciences

Teaching languages: Portuguese

Languages of tutoring support: Portuguese, English

Regime de Frequência: Presencial

Presentation

The Bioinformatics CU addresses the main DNA and protein sequence databases and explores several tools to analyse molecular information. Different types of bioinformatic analyses are used, from molecular phylogeny to genome sequencing data analysis.

Sustainable Development Goals

Educação de qualidade - Assegurar a educação inclusiva, e equitativa e de qualidade, e promover oportunidades de aprendizagem ao longo da vida para todos.

Learning Goals

It is intended that the students recognize bioinformatics applications in molecular biology, in particular in the understanding of the various cell phenomena, in prokaryotes or in eukaryotes. It is intended that students analyze DNA sequences as genes coding for proteins or RNAs. Develop the ability to search sequence databases. Students should identify ORFs-protein coding genes- in prokaryotes and eukaryotes. Students should analyze data resulting from genomes and transcriptomes projects. Develop the ability to use the online learning platform of the University of Évora (Moodle).

Introduction. The central paradigm of bioinformatics.

1. Sequences Databases
Editing and depositing sequences
Databases (NCBI Database, Ensembl, PDB)
Search databases

2. Analysis of DNA and RNA sequences
Analysis of genetic codes; codon frequency .
Identification of ORFs
Identification of promoters, terminators, etc.
Analysis of secondary structure of RNAs

3. Alignment of Sequences
Programs BLAST and Clustal
Identification of functional domains

4. Analysis of complete genomes
Annotation of sequences. RAST programs, Blast2GO
Analysis of categories of Clusters of Orthologous Genes (COG)
Analysis of interactive genes

5. Analysis of prokaryotic Genomes
Identification of genes and operons

6. Analysis of eukaryotic Genomes
Identification of introns, regulatory regions

7. Molecular phylogenetic analysis
Types of phylogenetic trees
Construction methods of trees (UPGMA, Neighbor-joining, Maximum likelihood, Maximum parsimony)

8 Analysis of transcriptomic data
Data Analysis of Microarrays, EST.

9. Bioinformatics of Proteins
Identification of functional domains
Prediction of secondary structure and cellular localization

Teaching Methods

This curricular unit includes theoretical and theoretical-practical classes, taught in rooms equipped with computers.
The lectures will cover the principles and fundamentals of the bioinformatics tools to be used. Whenever necessary, the key concepts of molecular biology will be recalled so that the bioinformatics tools can be understood.
In theoretical-practical classes, students will solve problems/exercises involving the use of bioinformatics tools available online or freely available software aimed at analysing DNA, RNA or protein sequences.
The Moodle platform will be used to provide all the necessary material for the classes and also during the assessment.

Assessment

Continuous Assessment: 3 written tests in which the contents of the theoretical classes (50%) and the theoretical-practical classes (50%) are assessed. The 3 tests have equal weight in calculating the final grade.
Final Assessment: 2 written tests assessing the contents of the lectures (50%) and the theoretical-practical classes (50%). One test has a weight of 1/3 and the other has a weight of 2/3 of the final grade.