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





Responsible teacher

Ricardo Parreira


Weekly - 6

Total - 39

Teaching language



Not applicable


• Claverie, J.-M., Notredame, C. (2007). Bioinformatics for Dummies. 2nd Edition. Wiley Publishing Group.
• Lesk, A. (2008). Introduction to Bioinformatics. 3rd Edition. Oxford Press.
• Salemi, M. Vandamme, A.-M. (ed). (2003). The Phylogenetic Handbook. Cambridge University Press.
• Higgs, P.G. Attwood, T.K. (2005). Bioinformatics and Molecular Evolution. Blackwell Science, Ltd.
• Gibson, D.G., Glass, J.I, Lartigue, C, et al. (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science, 329 (5987): 52-56.

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 evaluation process sets on a two-part (sequence analysis/phylogenetic reconstruction) group-written assay, in the form of a scientific paper, which should be a scientifically accurate, concise digest of the results obtained. The students will be guided in their assay preparation in the form of tutorial sessions. Class performance, participation and interest will also be evaluated.

Subject matter

I.Introduction to bioinformatics.
II.Reference searches using public databases.
III.Presentation of the GenBank, EMBL, UniProtKB, SwissProt, PDB, InterPro and Pfam databases.
IV.Sequence formats and sequence annotation.
V.Concepts of homology, positional homology, and similarity.
VI.Types of nucleotide substitutions. Nucleotide and protein sequence alignments and their use: multiple vs local, pairwise vs global.
VII.Construction of multiple sequence alignments using progressive (Clustal) and iterative algorithms (MAFFT, Muscle).
VIII.Phylogenetic trees, evolutionary models, and corrected genetic distance matrixes. Phylogenetic reconstruction (neighbor-joining and maximum likelihood).
IX.Assessment of tree topology stability.
X.Analysis of mosaics.
XI.Exploratory analysis of raw sequence data (composition, RNA and protein secondary structure), protein domains, properties and function, identification of genes in a sequence).


Programs where the course is taught: