Bioinformatics
- Cours (CM) 14h
- Cours intégrés (CI) -
- Travaux dirigés (TD) 10h
- Travaux pratiques (TP) 2h
- Travail étudiant (TE) -
Langue de l'enseignement : Anglais
Description du contenu de l'enseignement
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.
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 à acquérir
- 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, lectures recommandées
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.
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.
Contact
Responsable
Odile Lecompte
