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COMBINED COURSE BIOINFORMATICS - BIOINFORMATICS MODULE 2
PAOLO MARIANI

Seat Scienze
A.A. 2016/2017
Credits 4
Hours 32
Period 1^ semestre
Language ENG
U-gov code SM04 5S347

Prerequisites

General knowledge of genetics and molecular biology. Basic mathematical, chemical and physical concepts.

Development of the course

Lectures are provided as well as at least 2 CFU of practical exercises in the computer lab (carried out individually or in small groups).

Learning outcomes

Knowledge:
The aim of the course in bioinformatics is to provide an introduction to the knowledge and use of bioinformatics tools freely available on the World Wide Web, and useful for the analysis of nucleic acid and protein sequences and more generally for the evaluation of data available in biological databases.

Ability to apply the knowledge:
At the end of the course, the student will be able to examine the information available in biological databases and to use some of the most important bioinformatics tools to study nucleotide and protein sequences.

Soft skills
Individual and group exercises in the "Informatics Lab" contribute to improving the degree of autonomy of the student and his ability to work in teams and communicate with others. Moreover, practice exercises contribute to improving student computer skills.

Program

Principles of protein structure (secondary, tertiary and quaternary structure); Protein sequence databases; Sequence motif databases; Protein structure databases (PDB); Protein structure representation and view; Structure alignment; Searching 3D Databases; Classifying 3D shapes; Protein secondary structure analysis: defining a secondary structure element, methods for predicting secondary structure; Experimental methods for protein structure determination: X-ray crystallography and nuclear magnetic resonance NMR; Protein tertiary structure modeling: Basic concepts, Protein folding and dynamic simulation, Modeling protein side-chains, Homology modeling, Folding recognition, Threading, Ab initio modeling.

Development of the examination

Methods for assessing learning outcomes:
Oral examination, common for the I and II modules, with registration in the own private area.

Criteria for assessing learning outcomes: 
The final exam consists in the evaluation of a written report prepared by the student (the analysis of a protein using the bioinformatics tools available on the web) and an oral test to demonstrate the ability to use advanced information tools (databases, software packages) for genetics and biology.

Criteria for assessing learning outcomes: 
The final mark is assigned on the basis of the written report (insufficient, sufficient, good, very good) and of the oral exam through questions at low, medium, and high difficulty

Criteria for conferring final mark:
The final mark is assigned on the basis of the following 4 items:
1. the quality of the written report (efficacy, completeness, adherence to specifications, evaluation and analyses of the relevant information);
2. the understanding of all the material presented in the report, 
3. the skill demonstrated in biological database interrogation and in the use of related software,
4. the demonstration of subject competences and of clarity and appropriateness of technical and scientific language used.
The final mark is also assigned considering the student's ability to link the topics covered during the course among themselves and with topics of other courses already attended by the student.

Recommended reading

S. Pascarella e A. Paiardini, Bioinformatica, Zanichelli, Bologna.
DE. Krane e ML Raymer, Fondamenti di Bioinformatica, Pearson
A.M. Lesk, Introduzione alla Bioinformatica, McGraw-Hill Companies
D.W. Mount, Bioinformatics: sequence and genome analysis, Cold Spring Harbor Lab. Press.
C. Gibas, and P. Jambeck, Developing bioinformatics computer skills, O´Reilly, Cambridge
Slides provided during the course.
 

Courses

• Biologia molecolare e applicata