Application of bioinformatic methods 6.1-AoBM
A. Lecture: Essential bioinformatics. Molecular databases as sources of DNA sequences used in various fields of life sciences. Analyses of mitochondrial and nuclear DNA. DNA polimorphism. Molecular markers in phylogenomics, phylogeography, ecology, conservation biology, forensic biology, medicine and biodiversity studies. Computer programms enabling the use of bioinformatic data in various fields of life sciences.
B. Laboratory: Computer programms and bioinformatic databases in phylogenomic and phylogeographic analyses. Haplotype analyses. Procedures of downloading the DNA sequences from GenBank. Sequence alignments and analyses. Substitution model selection. Tree construction using different algorithms. Oral presentation of results of computer analyses and simulations (accompanied by the electronic presentation).
C. Conversatory: Mitochondrial, chloroplast and nuclear genomes, their structure, function and evolution. DNA sequences alignment. Molecular clock and its calibration. Usefulness of the molecular clock in phylogenomics and phylogeography. Molecular markers in phylogenomics, phylogeography, conservation biology and biodiversity studies – examples. Computer programms used in phylogenomics and phylogeography. Application of bioinformatic methods in studies on fossils. Basics of the structural bioinformatics.
Type of course
Course coordinators
Learning outcomes
Knowledge
K_W01_/ P7S_WG recognizes research problems from the borderline of biological sciences K_W02_ /_ P7S_WG interprets the complexity of processes and phenomena in nature, the solution of which requires an interdisciplinary approach
K_W04_/_ P7S_WG performs multi-aspect comparative analysis of the molecular, cellular and physiological mechanisms of the functioning of organisms
K_W05_/_ P7S_WG describes the rules and mechanisms of molecular and cellular development of organisms, including embryogenesis
K_W12_/_ P7S_WG recognizes the dynamic development of biological sciences
K_W15_/_ P7S_WG searches and uses specialized bioinformatics tools, useful in solving problems studiowanej specjalności nauk biologicznych
Skills
K_U02_/ _ P7S_UK fluent in the scientific literature of the biological specialty he is studying in his mother tongue, and speaks English at a level B2+
K_U03_ /_ P7S_UW demonstrates the ability to critically analyze and select biological information, especially from electronic sources
K_U05_ /_ P7S_UW uses statistical methods and IT techniques and tools to describe biological phenomena and analyze specialized statistical data
K_U07_/_ P7S_UW critically confronts biological information from various sources and draws justified conclusions on this basis
K_U08_ /_ P7S_ presents critically the research work in the field of selected specialty in biological sciences with the use of verbal communication and multimedia
Social competencies
K_K01_/_ P7S_KK aware of the complexity of biological phenomena and processes
K_K04_ / _ P7S_KK recognized sources of scientific information and using the principles of critical reasoning in resolving practical problems
K_K06_ /_ P7S_KK systematycznie aktualizuje wiedzę biologiczną i informacje o jej praktycznych zastosowaniach zastosowaniach
Assessment criteria
Conditions to get credits for:
A. Way of final evaluation:
• lectures: a grade
• laboratory: a grade
• conversatory: a grade
B. Form of testing:
• lecture: final written test (including open and closed questions)
• laboratory: oral presentation of results of computer analyses and simulations (accompanied by the electronic presentation)
• conversatory: oral presentations based on literature studies accompanied by the electronic presentation
C. Basic criteria
• L: positive rating over 50% of points scored (in the examination test)
• Lab: evaluation of results obtained during computer analyses
Conv: evaluation of the oral presentations accompanied by the electronic presentation
Bibliography
A. obligatory literature:
A.1. used during lectures and laboratory sessions
- Xiong J. Essential bioinformatics. Cambridge University Press, 2006.
- Freeland J.R. Molecular ecology. John Wiley & Sons Ltd., 2005
- Hall B.G. Phylogenetic trees made easy: A how-to manual. Third edition. Sinauer Associates Inc., 2008.
- specialised literature.
A.2. lectures for self-study – as above
B. additional literature
- Avise J.C. Phylogeography: the history and formation of species. Harvard University Press, 2001.
- Higgs P.G., Attwood T.K. Bioinformatics and Molcular Evolution. Blackwell Science Ltd., 2005.
- specialised literature.
Additional information
Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system: