The course is aimed to provide information and tools to solve the most classic issues of computational biochemistry and bioinformatics such as consultation of databases available on the web, sequence alignment, molecular evolution, identification and searching of functional patterns, the prediction of the protein structure and skills required to analyze genomes and decipher the information contained in them. The course also aims to familiarize the student 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 computational biochemistry and bioinformatics

-data

-post-genomic era

-databases of nucleic acids

-databases of protein

-databases of structure

-databases derived

-database integration

-quality of data

-representation of data

-architecture of proteins

-analysis of genomic sequences: concepts and principles

-sequencing of a genome

-searching gene

-statistical methods for finding genes

-site-specific scoring matrices

-artificial neural networks

-Markov Model and Hidden Markov Model

-comparative genomics

-evolution of proteins: concepts and principles

-molecular evolution

-alignment of two sequences similar

-similarity matrices

-PAM matrices

-BLOSUM metrices

-penalization of insertions and deletions

-alignment algorithm

-multiple alignments

-adding sequences in an alignment preexisting

-phylogenetic trees

-searching in databases for similarity: concepts and principles

methods: FASTA and BLAST

Searching with profiles: PSI-BLAST

-analysis of an amino acid sequence: concepts and principles

Search pattern sequence

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

-secondary structure

-prediction of secondary structure

-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

-pharmacogenomics

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 with PC, both for the retrieval of biological data and for the use of programs that allow alignment of nucleotides and amino acids, choice of amplification primers, analysis of protein structures.

Teaching

Lectures and exercises on PC

Course books

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

Bioinformatics: an introduction.  Author: Ramsden, Jeremy.  Springer ed

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

Disabilità e DSA

Le studentesse e gli studenti che hanno registrato la certificazione di disabilità o la certificazione di DSA presso l'Ufficio Inclusione e diritto allo studio, possono chiedere di utilizzare le mappe concettuali (per parole chiave) durante la prova di esame.

A tal fine, è necessario inviare le mappe, due settimane prima dell’appello di esame, alla o al docente del corso, che ne verificherà la coerenza con le indicazioni delle linee guida di ateneo e potrà chiederne la modifica.