2023
Biocomputing
Name: Biocomputing
Code: BIO12359L
6 ECTS
Duration: 15 weeks/156 hours
Scientific Area:
Biological Sciences
Teaching languages: Portuguese
Languages of tutoring support: Portuguese
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
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).
Contents
1. Sequences databases
Editing and depositing sequences
Searching databases
2. Analysis of DNA and RNA sequences
Genetic codes and codon frequency
Identification of ORFs, promoters, terminators
Analysis of secondary structure of RNAs
3. Alignment of sequences
Programs Clustal and BLAST
Identification of functional domains
4. Analysis of genomes
Annotation of sequences
Analysis of Clusters of Orthologous Genes
Identification of genes and operons
Identification of introns and regulatory regions
5. Molecular phylogenetic analysis
Types of phylogenetic trees
Tree-building methods
6. Analysis of transcriptomic data
Analysis of microarrays data
7. Bioinformatics of Proteins
Identification of functional domains
Prediction of secondary structure and cellular localization
8. Introduction to the Linux command line
The operating system, file system and command line interface
Handling and processing text files
Tools for processing Next Generation Sequencing data
Editing and depositing sequences
Searching databases
2. Analysis of DNA and RNA sequences
Genetic codes and codon frequency
Identification of ORFs, promoters, terminators
Analysis of secondary structure of RNAs
3. Alignment of sequences
Programs Clustal and BLAST
Identification of functional domains
4. Analysis of genomes
Annotation of sequences
Analysis of Clusters of Orthologous Genes
Identification of genes and operons
Identification of introns and regulatory regions
5. Molecular phylogenetic analysis
Types of phylogenetic trees
Tree-building methods
6. Analysis of transcriptomic data
Analysis of microarrays data
7. Bioinformatics of Proteins
Identification of functional domains
Prediction of secondary structure and cellular localization
8. Introduction to the Linux command line
The operating system, file system and command line interface
Handling and processing text files
Tools for processing Next Generation Sequencing data
Teaching Methods
This course inconcludes theoretical and theoretical-practical classes, which will take place in classrooms equipped with computers.
In the theoretical classes, the principles and fundaments of different bioinformatic tools will be discussed. Whenever necessary, the key concepts of molecular biology that allow the comprehension of the bioinformatics tools will be reviewed.
In the theoretical-practical classes, the students will resolve problems/exercises that imply the use of bioinformatic tools available online or open source software, specific for the analysis of DNA, RNA or protein sequences.
The Moodle platform will be used to make available all the classes material, but also with evaluation purposes.
In the theoretical classes, the principles and fundaments of different bioinformatic tools will be discussed. Whenever necessary, the key concepts of molecular biology that allow the comprehension of the bioinformatics tools will be reviewed.
In the theoretical-practical classes, the students will resolve problems/exercises that imply the use of bioinformatic tools available online or open source software, specific for the analysis of DNA, RNA or protein sequences.
The Moodle platform will be used to make available all the classes material, but also with evaluation purposes.
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%)
Final Assessment: 2 written exams where the contents of the theoretical classes (50%) and theoretical-practical classes (50%)
Teaching Staff
