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.

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: Concepts and principles

-secondary structure and prediction of secondary structures

-prediction of long-range contacts

-prediction of molecular complexes: the docking

-stages of the procedure for modeling by homology

-selection of the protein template

-sequence alignment and reliability

-loops

-modelling of the side chains

-optimization model

-accuracy of a model for homology

-models built manually and automatically

-methods of fold recognition

-methods based on profiles

-threading methods

-library of fold

-energy calculations

-evaluation of the energy of a protein

-energy minimization

-molecular dynamics

-genetic algorithms

-methodologies combined

-transcriptomics

-proteomics

-structural genomics

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

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

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

Teaching

Lectures and computer exercises 

Attendance

no

Course books

BIOINFORMATICA -Dalla sequenza alla struttura delle proteine - S.Pascarella e A.Paiardini - Zanichelli (2010)

FONDAMENTI DI BIOINFORMATICA - Manuela Helmer Citterich, Fabrizio Ferrè, Giulio Pavesi, Graziano Pesole, Chiara Romualdi (2018)

BIOINFORMATICS: METHODS AND APPLICATIONS: (Genomics, Proteomics and Drug Discovery). Authors: S. C. RASTOGI, NAMITA MENDIRATTA, PARAG 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

Disability and Specific Learning Disorders (SLD)

Students who have registered their disability certification or SLD certification with the Inclusion and Right to Study Office can request to use conceptual maps (for keywords) during exams.

To this end, it is necessary to send the maps, two weeks before the exam date, to the course instructor, who will verify their compliance with the university guidelines and may request modifications.

Course books

BIOINFORMATICA - Dalla sequenza alla struttura delle proteine - S.Pascarella e A.Paiardini - Zanichelli (2010)

FONDAMENTI DI BIOINFORMATICA - Manuela Helmer Citterich, Fabrizio Ferrè, Giulio Pavesi, Graziano Pesole, Chiara Romualdi (2018)

BIOINFORMATICS: METHODS AND APPLICATIONS: (Genomics, Proteomics and Drug Discovery). Authors: S. C. RASTOGI, NAMITA MENDIRATTA, PARAG 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

Disability and Specific Learning Disorders (SLD)

Students who have registered their disability certification or SLD certification with the Inclusion and Right to Study Office can request to use conceptual maps (for keywords) during exams.

To this end, it is necessary to send the maps, two weeks before the exam date, to the course instructor, who will verify their compliance with the university guidelines and may request modifications.