The teaching is organized as follows:

Learning outcomes

The course will provide the theoretical and practical basis to understand and employ algorithms and programs currently used in Bioinformatics. Major biological databases will be introduced with a special focus on genomic, proteomic and biochemical information. The students will also be introduced to the most modern fields of structural bioinformatics and systems biology.

Program

Theoretical Module

- Overview of the main structural features of proteins and nucleic acids in relation to the concept of evolution. Introduction to biomolecular databases: online resources and their use

- Biological databases: organization and integration of information concerning: a) protein and nucleic acid sequences; b) biomolecular structures; c) bibliographic and scientific literature. Retrieve of specific information: use of limitations and Boolean operators.

- Sequence comparison and alignments: static and dynamic algorithms; substitution matrices (PAM,BLOSUM)
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- Search-algorithms: FASTA and BLAST; Smith-Waterman; Needleman-Wunsch; statistic significance for an alignment (z-score, expectation values and probability)

- Multiple sequence alignments: ClustalW, search on specific databases, other algorithms, PSI-BLAST

- Short introduction on philogenetic trees

- Introduction to Structural Bioinformatics: visualization and analysis of protein and nucleic acid 3D structures

- Methods to predict protein secondary structure elements starting from the sequence

- Introduction to Systems Biology: Spatial and temporal scales, static and dynamic models, mathematical frameworks, introduction on signal transduction networks


Laboratory Module

- Introduction to Linux

- NCBI databases: Entrez interface, Gene, UniGene, Protein, Uniprot and EBI

- Single and multiple sequence alignments, score matrices, optimal methods; online resources and spreadsheets

- BLAST,PSI-BLAST and BLAT: online tools and their use

- Tools for multiple alignments, the Homologene databank, computation and visualization of multiple alignments

- Tools for phylogenesis : Mobyle (Institut Pasteur and Phylogeny.fr)

- Introduction to PyMol and molecular visualization. Use of PSI-PRED and JPRED for predicting secondary structures from sequences

- Systems biology: numerical simulation of simple biochemical reactions. Building simple kinetic models by using SBOTOOLBOX2 for Matlab; application to G-potein signalling cycles.

Examination Methods

Written exam for both modules. The two marks will be averaged. Students can chose to prepare a presentation in groups of 3-4 students on a selected database, which will also contribute to the final mark.