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

Theoretical and practical classes (theoretical sessions and practical sessions of computational bioinformatics).
In Bioinformatic practical classes the students use tools and bioinformatics software for sequence analysis, including molecular phylogeny, etc.
By email, the teacher is in regular contact with students, and is ready to answer questions and provide advice to students on the bibliography, etc.

Evaluation
Theory: Exam or two frequencies; Practice: Examination and / or report

Assessment

Continuous Assessment: 3 written tests where the contents of theoretical classes (50%) and theoretical-practical classes (50%) are evaluated
Final Assessment: 2 written exams where the contents of the theoretical classes (50%) and theoretical-practical classes (50%)