OVERVIEW

The modern techniques of genome sequencing and analysis of protein sequences produce large amount of data that require the use of informatics technologies and of the web. The aim of this teaching Module is to illustrate the methods used for genome and protein analysis, the algorithms used in Bioinformatics, and the software applications of common usage. Teaching will be carried out through the extensive use of web servers.

AIMS AND CONTENT

LEARNING OUTCOMES

The modern techniques of genome sequencing and analysis of protein sequences produce large amount of data that require the use of informatics technologies and of the web. The aim of this teaching Module is to illustrate the methods used for genome and protein analysis, the algorithms used in Bioinformatics, and the software applications of common usage. Teaching will be carried out through the extensive use of web servers.

AIMS AND LEARNING OUTCOMES

At the end of the course the student will have to know the main existing databases and the softwares able to analyze the data they contain.

The student will also have to understand which are the most correct algorithms and softwares to be used for the analysis of specific genomic or protein sequences. He will also have to be able to analyze different sequences to solve problems that will be submitted to him and discuss the results obtained.

PREREQUISITES

The student must have the basic skills to surf the net, download files and material from the web, create excel and word files, capture images from the screen.

The student will also have to know well the structure of DNA and proteins, the three-letter and single-letter abbreviations of amino acids as well as knowing the definition of primary, secondary, tertiary and quaternary structure of proteins and functional domains of proteins.

TEACHING METHODS

Frontal lessons:

During the lectures, students will learn the theory behind database searching and the analysis of the information contained therein. Furthermore, the main softwares for sequence analysis and their operation will be shown.

Practical exercises:

During the practical exercises, exercises will be carried out to allow students to understand the the softwares that they will have to use during the exam.

Any Student with documented Specific Learning Disorders (SLD), or with any special needs, shall reach out to the Lecturer(s) and to the dedicated SLD Representative in the Department before class begins, in order to liase and arrange the specific teaching methods and ensure proper achievement of the learning aims and outcomes.

SYLLABUS/CONTENT

• Introduction to protein structure

• Databases and database search

• Alignment of protein sequences

• Softwares for protein analysis

• Introduction to phylogenetic analyzes

RECOMMENDED READING/BIBLIOGRAPHY

All the slides used during the lessons and other teaching material will be available on aul@web. In general, the notes taken during the lessons and the material on aul@web are sufficient for the preparation of the exam. The books listed below are suggested as supporting texts, but students can use other university-level bioinformatics texts as well, as long as they are editions published in the last 5 years.

S. Pascarella, A. Paiardini  - Bioinformatica. Zanichelli Ed.

P.M. Selzer, R.J. Marhöfer, O. Koch - Applied Bioinfomatics. Springer Ed.

J. Xiong  - Essential Bioinfomatics. Cambridge Ed.

TEACHERS AND EXAM BOARD

Exam Board

DAVIDE CERESA (President)

FRANCESCO PIACENTE (President)

LESSONS

Class schedule

The timetable for this course is available here: Portale EasyAcademy

EXAMS

EXAM DESCRIPTION

Written exam in which the student will have to solve problems using the theory and softwares learned during lectures and exercises.

ASSESSMENT METHODS

The student will have to show he is able to obtain information from the main databases, analyze them with the softwares described in class and comment the obtained results.