Università degli Studi di Urbino Carlo Bo / Portale Web di Ateneo


BIOINFORMATICS
BIOINFORMATICA

A.Y. Credits
2019/2020 8
Lecturer Email Office hours for students
Annamaria Ruzzo
Teaching in foreign languages
Course with optional materials in a foreign language English
This course is entirely taught in Italian. Study materials can be provided in the foreign language and the final exam can be taken in the foreign language.

Assigned to the Degree Course

Sanitary Nutritional and Environmental Biology (LM-6)
Curriculum: DIAGNOSTICA MOLECOLARE
Date Time Classroom / Location
Date Time Classroom / Location

Learning Objectives

The course is aimed to provide information and tools to solve the most bioinformatics classic issues such as consultation of databases available on the web, sequence alignments, molecular evolution, identification and searching of functional patterns, prediction of the protein structure and skills required to analyze genomes and decipher the information contained in them. The course also aims to familiarize students with solutions currently used by assessing potentialities and limits starting from biological problems.

Program

The course will address the following topics at various levels:

-concepts and principles of bioinformatics

-data

-post-genomic era

-databases of nucleic acids, proteins, structures

- derived databases

- the quality of data

-representation of data

-architecture of proteins

-analysis of genomic sequences: concepts and principles

-sequencing of a genome

-searching genes

-statistical methods for finding genes

-site-specific scoring matrices

-artificial neural networks and Hidden Markov Model

-comparative genomics

-evolution of proteins: concepts and principles

-molecular evolution

-alignment of two sequences searching similarity

-matrices for similarity

-PAM and BLOSUM matrices

-penalization of insertions and deletions

-alignment algorithm

-multiple alignments

-adding sequences in an preexisting alignment

-phylogenetic trees

-searching in a database for similarity: concepts and principles

-searching in databases with euristic methods : FASTA and BLAST

-searching with profiles: PSI-BLAST

-analysis of an amino acid sequence: concepts and principles

-searching pattern sequence

-predicting the three-dimensional structure of a protein: principles

-secondary structure and prediction of secondary structures

-stages of the procedure for modeling by homology

-selection of the protein template

-sequence alignment and reliability

-loops

-accuracy of a model for homology

-models built manually and automatically

-methods of fold recognition

-methods based on profiles

-library of fold

-transcriptomics

-proteomics

-structural genomics

Learning Achievements (Dublin Descriptors)

Students will acquire the following skills:

1- learning and discussing topics covered in class

2- proving to be able to solve problems starting from biological data found in the main biological databases and proving to be able to set up experiments in molecular biology according to the acquired data

3- knowing how to search in the literature medical / biological topics and crossing them with the data of databases biological

4- presenting  at the oral exam arguments of the course through a written paper (short thesis) in which it is simulated a searching of computational biochemistry chosen by the student

Teaching Material

The teaching material prepared by the lecturer in addition to recommended textbooks (such as for instance slides, lecture notes, exercises, bibliography) and communications from the lecturer specific to the course can be found inside the Moodle platform › blended.uniurb.it

Supporting Activities

The course includes classroom exercises on PC, both for the retrieval of biological data and the use of programs that allow nucleotides and amino acids alignment, choice of amplification primers, analysis of protein structures.


Didactics, Attendance, Course Books and Assessment

Didactics

Lectures and computer exercises 

Attendance

no

Course books

BIOINFORMATICS: METHODS AND APPLICATIONS: (Genomics, Proteomics and Drug Discovery). Authors: S. C. RASTOGINAMITA MENDIRATTAPARAG RASTOGI (2013)

Assessment

Oral examination together with an elaborate (thesis) which simulates a searching, in which a large part of the course topics will be addressed from a practical point of view

Additional Information for Non-Attending Students

Course books

BIOINFORMATICS: METHODS AND APPLICATIONS: (Genomics, Proteomics and Drug Discovery). Authors: S. C. RASTOGINAMITA MENDIRATTAPARAG RASTOGI (2013)

Assessment

Oral examination integrated with a  short elaborate (thesis) which simulates a research of biological data in public databases, where a large part of the course topics will be addressed from a practical point of view

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