Bioinformatics
Diplôme d'ingénieur de l'École supérieure de biotechnologie de Strasbourg (ESBS)Parcours Diplôme d'ingénieur en biotechnologie
Description
The course is devoted to the basic resources and tools used in the analysis of a gene or protein family. It presents the structuring of biological information as well as the essential methods and programs for sequence analysis. A large part of the course is devoted to practical work in the computer resource room.
Detailed content
- Biological databases: presentation of the main sequence databases and sequence-related databases, structuring of biological information, ontology.
- Comparison of 2 sequences: similarity and homology, score systems, dotplots, optimal alignments of 2 sequences, similarity searches (BLAST, BLAT).
- Multiple alignment: main algorithms and programs commonly used, quality of an alignment, applications of multiple alignment, patterns and profiles
- Molecular phylogeny: terminology, examples of phylogeny applications, tree construction methods, tree robustness estimation, web tools and resources.
Compétences visées
- Ability to use basic bioinformatics web resources
- Understanding of main sequence comparison algorithms
- Ability to interpret a multiple alignment, a phylogenetic tree and results of a similarity search
- Ability to use multidisciplinary knowledge and approaches
Bibliographie
Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.
Baxevanis, A.D., Bader, G.D., and Wishart, D.S. (2020). Bioinformatics (John Wiley & Sons).
Lecompte, O., Thompson, J.D., Plewniak, F., Thierry, J.-C., and Poch, O. (2001). Multiple alignment of complete sequences (MACS) in the post-genomic era. Gene 270, 17–30.
The UniProt Consortium, Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Agivetova, R., Ahmad, S., Alpi, E., Bowler-Barnett, E.H., Britto, R., et al. (2021). UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Research 49, D480–D489.
Yang, Z., and Rannala, B. (2012). Molecular phylogenetics: principles and practice. Nat. Rev. Genet 13, 303–314.