82312 - Bioinformatics

Learning outcomes

By the end of the course, students will understand the computational methods and tools underlying molecular- and systems-level investigation. They will acquire knowledge of the current landscape of biological and systems-oriented databases and the ability to retrieve information from deposited data. They will also become familiar with the main challenges of the post-genomic era, from genome and proteome annotation to the role of mutations in the function of biological systems, and with the analysis of genomic and proteomic data and of protein–protein and protein–DNA/RNA interactions. By the end of the laboratory module, students will be able to build on the knowledge acquired to carry out focused searches independently and solve selected relevant problems using bioinformatics methods.

Course contents

The course includes a 4-CFU theoretical module and a 2-CFU laboratory module.

 

Theoretical module

Introduction to bioinformatics and computational biology. Main biological data types and formats. Databases for sequences, genomes, proteins and three-dimensional structures; retrieval and interpretation of deposited information.

Similarity, identity and homology. Global, local and multiple-sequence alignments. Substitution matrices, gap penalties and basic principles of alignment algorithms. BLAST searches and interpretation of the main output parameters.

Genome and proteome annotation. Identification of coding regions, domains, motifs and protein families. Homology, orthology and paralogy. Basic principles of phylogenetic-tree reconstruction and interpretation.

The Protein Data Bank, organisation and visualisation of protein structures. Relationships among sequence, structure and function. Structure comparison and prediction and interpretation of the effects of mutations.

Introduction to RNA-seq and ChIP-seq analyses: aims, general analytical workflows and interpretation of the main results.

 

Laboratory module

The laboratory module includes practical problems concerning relationships among sequence, structure and function in proteins and nucleic acids, as an application of the theoretical module. It also provides familiarity with the main biological databases.

 

Students with learning disorders and\or temporary or permanent disabilities: please, contact the office responsible (https://site.unibo.it/studenti-con-disabilita-e-dsa/en/for-students ) as soon as possible so that they can propose acceptable adjustments. The request for adaptation must be submitted in advance (15 days before the exam date) to the lecturer, who will assess the appropriateness of the adjustments, taking into account the teaching objectives.

Readings/Bibliography

M. Helmer-Citterich, F. Ferrè, G. Pavesi, C. Romualdi, G. Pesole, Fondamenti di bioinformatica, Zanichelli, in Italian.

The textbook will be supplemented with teaching materials, database documentation and online resources made available through the Virtuale platform.

Teaching methods

Lectures and laboratory activities.

Lectures introduce the theoretical principles and include examples of database searches and interpretation of sequences, structures, phylogenetic trees and post-genomic data, including RNA-seq and ChIP-seq results.

The practical module involves the application of selected tools and resources introduced in the theoretical module.

Assessment methods

Learning is assessed through a final written examination designed to verify the acquisition of the expected knowledge and skills. The written examination consists of multiple-choice questions and open-ended questions. The total available score is higher than 30, allowing students to obtain honours. The examination is passed with a score of at least 18/30.

The grade is combined with those of the other components of the Integrated Course according to the procedures established for the course.

 

Use of AI: With regard to the final assessment of learning, the use of AI is prohibited. Any use of AI will be considered a violation of academic integrity.

Teaching tools

PC, Internet access, projector and whiteboard. Biological databases, online bioinformatics tools and the Virtuale platform for distributing teaching materials. The practical module takes place in the teaching bioinformatics laboratory.

Office hours

See the website of Andrea Vannini

See the website of Fabrizio Ferrè