Bioinformatics and biological databases (2019/2020)

Course code
Nicola Vitulo
Academic sector
Language of instruction
Teaching is organised as follows:
Activity Credits Period Academic staff Timetable
Modulo 1 3 II semestre Nicola Vitulo

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Modulo 2 3 II semestre Valerio Marino

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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 con-tained 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 align-ments.


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.

Assessment methods and criteria

The exam covers both the theoretical part (module 1) and the laboratory part (module 2).
Both parts will be assessed during a single exam.
The exam on the theory part consists of a written test (typically 4 open questions) which aims to verify the level of knowledge acquired relating to the topics covered in the course.
The student must demonstrate to have understood the functioning and application of the main bioinformatics programs and approaches explained in class.
The part relating to the exercises will be carried out on the computer immediately after the written test. Two exercises will be provided which will be solved by putting into practice the skills acquired during the laboratory. The student will also have to demonstrate his ability to interpret the result of the programs studied during the course.

Reference books
Activity Author Title Publisher Year ISBN Note
Modulo 1 Stefano Pascarella e Alessandro Paiardini Bioinformatica Zanichelli 2011 9788808062192
Modulo 2 Stefano Pascarella e Alessandro Paiardini Bioinformatica Zanichelli 2011 9788808062192