Bioinformatics

Bioinformatics

Teachers: Silvia Bione, Davide Sassera, Giuseppe D’Auria
Year: 2018/2019
ECTS: 6
SSD: ING-INF/06

Course content

Objectives
Aim of the course is to provide students with the basic knowledge of bioinformatic methodologies, tools and approaches that are essential to integrate molecular biology and genetics studies and researches.

Programme
The course is structured in three modules, the first focused on bioinformatics resources available on the web, the second focused on bioinformatics of sequencing, the third on the R environment.

Part 1:
Functions and goals of Bioinformatics
NCBI and EBI sites
Query tools for integrated databases
Sequence comparison: basic notions and alignment tools.
Multiple sequences alignment.
Genome Browsers.
Regulatory elements in genome browsers.
Transcriptional profiles in genome browsers and database.
Bioinformatic analysis of alternative splicing.
Bioinformatic analysis of microRNA targets.
Tools for Data Mining

Part 2:
Bioinformatics for genomics.
The Linux terminal.
Bioinformatic files formats.
Genome assembly and annotation.
Comparative genomics and phylogeny.
Transcriptomics.
Metagenomics.

Part 3:
Introduction to the R environment.
Basic R concepts.
Creation of graphs and plots.
Database management.
Basics of statistics in R.

Laboratories for practical lessons
Finding information in biomedical databases. Tools for sequence comparison. The human UCSC genome browser. The architecture of regulatory elements. Making SNPs and repetitive sequences make sense. Data mining in gene lists. Analysis of gene regulation: alternative splicing and microRNA analysis. The basics of BASH usage. Managing files. Genome quality control and assembly. Genome annotation and comparison. Basics phylogenetic reconstructions.

Bibliography
– Lesk A. Introduction to bioinformatics Oxford Univ. Press, ed.
– Westhead DR, Parish JH & Twyman RM. Bioinformatics (Instant notes). Taylor and Francis, ed.
– NCBI Help Manual (http://www.ncbi.nlm.nih.gov/books/NBK3831/)

 

Teaching Material: teaching material for Bioinformatics will be provided via Facebook