Teaching code

4S02701

Credits

6

Coordinator

Nicola Vitulo

Language

Italian

Scientific Disciplinary Sector (SSD)

BIO/10 - BIOCHEMISTRY

Moodle Seminars 0

The teaching is organized as follows:

Learning outcomes

The course aims to introduce the student to bioinformatics, providing basic notions basically fo-cused on the analysis of both nucleotide and protein sequences. The course will provide both theo-retical and practical bases of algorithms, programs and methods for searching and analyzing se-quence 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.

Program

The class is divided into two modules, one theoretical and one more practical which takes place through exercises directly on the computer. The topics covered by the two modules are the same, allowing students to put into practice the notions that will be studied from a theoretical point of view.

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.

Examination Methods

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.