APPLIED BIOINFORMATICS

Second cycle degree in BIOTECHNOLOGIES FOR FOOD SCIENCE (Ord. 2017)

Campus: LEGNARO (PD)

Language: English

Teaching period: First Semester

Lecturer: CRISTIAN TACCIOLI

Number of ECTS credits allocated: 10


Syllabus
Prerequisites: The students need to know the main characteristics of DNA structure, amino acids, genes and genomes. A basic knowledge of personal computers is also required (Windows, Mac or Linux).
Examination methods: There will be a written Bioinformatics examination at the end of the course.
Course unit contents: PRINCIPLES OF BIOINFORMATICS USING PYTHON

Basics of Python programming (for/while loop, if/else statements, lists, tuples, dictionaries, regular expressions, lambda functions, list comprehensions, open/read files, directories, classes and objects). How to use Numpy, Scipy, matplotlib and Biopython. Parsing data files. Introduction to Alignment algorithms, Clustering and PCA.


MOLECULAR EVOLUTION, PHYLOGENETICS AND PHYLOGENOMICS

Principles of molecular evolution, phylogenetics and phylogenomics. Multiple alignments: a phylogenetic context. Methods of phylogenetic reconstruction: the main computer packages. Types of selection acting at DNA and amino acid level: local and web bioinformatic tools. Prediction of RNA and protein structures and their usage in molecular evolution, phylogenetics and phylogenomics. Bioinformatics approaches to species identification included the analysis of gene orders.