Bioinformatics and biological databases (2016/2017)

Course code
4S02701
Name of lecturer
Nicola Vitulo
Coordinator
Nicola Vitulo
Number of ECTS credits allocated
6
Academic sector
BIO/10 - BIOCHEMISTRY
Language of instruction
Italian
Location
VERONA
Period
II sem. dal Mar 1, 2017 al Jun 9, 2017.

Lesson timetable

II sem.
Day Time Type Place Note
Wednesday 11:30 AM - 1:30 PM lesson Lecture Hall D  
Wednesday 2:30 PM - 4:30 PM lesson Laboratory Alfa  

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.

Syllabus

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

Written with open question regarding the argument of the course

STUDENT MODULE EVALUATION - 2016/2017