Bioinformatics

Objectives

After this unit, students should be able to:
1. Recognition of the potential use of bioinformatics in the field of biomedical sciences.
2. Application of the acquired knowledge to the resolution of complex problems, including: the construction of sequence contigs from independent chromatograms, the identification of genes in a sequence, the critical use of public databases including homologous sequence-searches using different algorithms, and the exploratory analysis of a proteins’ structure and biochemical properties.
3. Demonstration of acquisition of general basic skills in the domain of bioinformatics, in particular in fields of molecular phylogeny and phylogenetic inference, and exploratory analysis of raw sequence data.
4. Demonstration of synthesis and critical analysis skills towards the preparation of a written assay in the form of a scientific paper.

General characterization

Code

9512025

Credits

3

Responsible teacher

Ricardo Parreira

Hours

Weekly - 6

Total - 39

Teaching language

Portuguese

Prerequisites

Not applicable

Bibliography

• Claverie, J.-M., Notredame, C. (2007). Bioinformatics for Dummies. 2nd Edition. Wiley Publishing Group.
• Higgs, P.G. Attwood, T.K. (2005). Bioinformatics and Molecular Evolution. Blackwell Science, Ltd.
• Lemey, P., Salemi, M., Vandamme, A.-M. (ed). (2009). The Phylogenetic Handbook. 2nd edition. Cambridge University Press.
• Lesk, A. (2020). Introduction to bioinformatics. 5th revised edition. Oxford University Press.

Teaching method

In most classes, a theory/practical teaching approach will be used. Theoretical concepts will be taught using expository methods, based on Powerpoints. All classes will include the use of computers for the resolution of exercises or the access to public databases.

Evaluation method

The assessment of knowledge will be essentially based on the presentation (in a group, in the 1st evaluation period) of a report in the format of a scientific article, and it is expected that students will be able to communicate their conclusions clearly, critically and scientifically. correct. Most tutorial classes will guide students in preparing their assessment. This (writing) will include two components: analysis (annotation) of a nucleotide sequence and the reconstruction of phylogenies based on analysis of previously provided nucleotide sequence alignments. The participation/interest shown in the classes will also be evaluated and may cause the students' classification to fluctuate up to a maximum of 2 values, in relation to the classification obtained in the 1st season (by the group). The evaluations in the 2nd season, unlike what happens in the 1st, will be done individually.

Subject matter

Analysis of chromatograms relating to sequencing carried out by the Sanger method. Editing "raw" sequences and building contigs. Formats and annotation of nucleotide sequences. Concept of homology, positional homology, and similarity. Types of Nucleotide Substitutions. Nucleotide or amino acid sequence alignments and their applications: global vs local, paired vs multiple alignment. Construction of multiple sequence alignments: progressive (Clustal) and iterative (MAFFT, Muscle) algorithms. Phylogenetic trees, evolutionary models and corrected genetic distances. Reconstruction of phylogenies: neighbor joining vs maximum likelihood. Robustness of a tree topology. Mosaic analysis. Composition (G+C), structure of RNA molecules and proteins, physical DNA mapping, gene research. Use of several tools in order to identify, characterize, analyze the possible function of proteins.

Programs

Programs where the course is taught: