Learning objectives
Knowledge and understanding: The course is primarily aimed at the acquisition of practical skills in the use of computers in Biology. Students will be taught the basic theoretical concepts necessary for an understanding of computer applications and bioinformatics.
Applying knowledge and understanding: through practical exercises under the guidance of the teacher, the students will have the opportunity to acquire practical skills on how to use open-source personal productivity software, and the most important bioinformatics applications.
Communication skills: through examples, students will learn how to report the results of computer analysis in a written report consisting of text and images, and how to organise their results in a multimedia presentation
Prerequisites
Elementary knowledge of Biology at the molecular level. Basics of computer use.
Course unit content
The first part of the course will address basic concepts about the use of computer and file management, as well as practical notions of the use of operating systems with graphical interface. Exercises will be carried out on applications for word processing, spreadsheets, multimedia presentations
The second part of the course will introduce the areas of bioinformatics and discuss the analysis of the sequences and structures of DNA and proteins. Students will be made familiar with the main databases of biological macromolecules and the most common techniques of bioinformatics analysis.
Full programme
Argomenti del corso:
Abilità informatiche
Concetti di base: significato e ambiti dell'informatica.
Uso del computer e gestione dei file: nozioni pratiche dell'utilizzo di sistemi operativi con interfaccia grafica.
Applicazioni di uso generale: nozioni pratiche di elaborazione testi, utilizzo fogli di elettronici, preparazione di presentazioni multimediali.
Reti informatiche: nozioni pratiche di utilizzo del World Wide Web.
Abilità bioinformatiche
Introduzione alla bioinformatica: significato e ambiti della bioinformatica. Oggetti della bioinformatica: sequenze di DNA e proteine,strutture di DNA e proteine. Evoluzione nel tempo dell'informazione biologica.
Banche dati di sequenze biologiche: definizione e scopo delle banchedati; principali banchedati di DNA (GenBank, DDBJ, EMBL) e di proteine (SwissProt, Pir). Interrogazione e consultazione delle banchedati. Sintassi del formato FASTA per le sequenze.
Confronto di sequenze: significato e scopi dell'allineamento di sequenze; allineamento a coppie. Algoritmi locali e globali di allinemanto. Penalita per l'inserimento gap e per allungamento gap. Matrici di sostituzioni aminoacidiche. Uso dei programmi Needle e Water.
Ricerca di omologia: significato dell'omologia. Misure della significatività dell'allineamento. Programmi per la ricerca di omologia in bancadati. Uso del programma Blast e lettura del risultato della ricerca di omologia.
Allineamento multiplo e filogenesi: utilizzi dell'allinemento multiplo. Uso del programma ClustalX. Visualizzazione dell'allineamento multiplo. Uso del programma GeneDoc. Ricostruzione filogenetica con l'algoritmo di neighbor-joining implementato in Clustal. Visualizzazione di alberi filogenetici con il programma Treeview
Predizione delle caratteristiche biochimiche delle proteine: catteristiche chimico-fisiche delle proteine. Uso del programma ProtParam. Predizione della localizzazione cellulare delle proteine. Uso dei programmi PSort e SignalP. Struttura delle proteine. Consultazione della banca dati di strutture PDB. Visualizzazione delle strutture con il programma Rasmol
Bibliography
Anna Tramontano: Bioinformatica. Zanichelli ed.
Teaching methods
The lessons of computer skills will be carried out mainly through practical exercises involving the use of computers by students. Students will learn the use of software for personal productivity: word processing, spreadsheets, and multimedia presentations.
Part of the lectures on bioinformatics skills will focus on theoretical arguments through a discussion of the basic concepts of the subject. The lectures will be interposed with practical exercises directed to the use of the most common bioinformatics applications. During these lessons, students will be trained to search for biological information in the databases and to solve the most common problems of sequence analysis.
During the practical exercises students will be able to follow step by step the use of the computer by the teacher and to replicate operations and controls on individual workstations.
Assessment methods and criteria
To check the general skills of the students, each student will present to the teacher a scientific report including text and figures, a spreadsheet table, and a short multimedia presentation.
Bioinformatics skills will be tested through an individual test in which the student will provides the solution of some biological problems through bioinformatics applications. An understanding of the basic concepts of bioinformatics will be verified through a short interview.
Other information
The course makes use of a classroom for the practical calculation equipped with 35 workstations connected to the Internet and equipped with general and bioinformatics programs discussed during the course. Only applications and programs in the public domain will be used during the course.
