Bioinformatics and biological databases (2018/2019)

Course code
Name of lecturer
Nicola Vitulo
Nicola Vitulo
Number of ECTS credits allocated
Academic sector
Language of instruction
II semestre dal Mar 4, 2019 al Jun 14, 2019.

Lesson timetable

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Learning outcomes

The course aims to introduce the student to bioinformatics, providing basic notions basically focused on the analysis of both nucleotide and protein sequences. The course will provide both theoretical and practical bases of algorithms, programs and methods for searching and analyzing sequence data contained in biological databases.
At the end of the course students will be able to:

Navigate among different biological databases and know how and where retrive the data
Analyze sequence data by searching similarity in database
Compare, analyze and manage sequence data using different types of programs for sequence alignments.


1. Introduction to bioinformatics

2. Biological databases: primary and secondary databases, search methods in biological databases.

3. Substitution matrix BLOSUM and PAM

4. Introduction to pairwise sequence alignment: dot matrix, algorithm based on dynamic programming (Smith-Watermann, Needlman-Wunsch) , heuristic programs (BLAST and FASTA)

5. Multiple alignments: introduction to multiple alignment algoritms (clustalW and T-Coffee). Positional weight matrices, PSI-BLAST and methods based on Hidden Markov Model (HMM)

6. Introduction to phylogenetic analysis and phylogenetic trees

7. Structural biology: computational methods to study secondary and tertiary protein structure.

Reference books
Author Title Publisher Year ISBN Note
Stefano Pascarella e Alessandro Paiardini Bioinformatica Zanichelli 2011 9788808062192

Assessment methods and criteria

The exam consists of a written verification (usually six open question about theory and one question about the laboratory part) of the level of knowledge regarding the argument of the course. The student must demonstrate understanding of the method and application of the major bioinformatic programs and approaches learned during the course. The student will also have to demonstrate how to interpret the results of the programs studied during the course.