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:
Concepts and principles of bioinformatics
Data 
The quality of data 
The representation of data
Databases of nucleic acids, proteins, and protein structures
The primary secondary and specialized databases
The integration of databases

The analysis of genomic sequences: concepts and principles
The search for genes in databases
Statistical methods for gene searching
Neural networks in bioinformatics
Hidden Markov Model
Comparative genomics

The evolution of proteins: Concepts and principles
The molecular evolution of proteins

Alignment of two sequences
Global, local, dot-plot alignments
Similarity matrices :PAM and BLOSUM
The penalty of insertions and deletions in alignments
The alignment algorithm
Multiple alignments
Phylogenetic trees

Searching databases for similarity: Concepts and principles 
The FASTA and BLAST methods 
Profile searches: PSI-BLAST 
Sequence pattern search 

The prediction of the secondary structure of proteins
Tertiary structure prediction
The stages of the homology modeling procedure 

Protein modeling
Model optimization 
Accuracy of a model by homology 
Automatically constructed models 

The fold recognition methods
Profile-based methods 

Translated with DeepL.com (free version)

no

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 nucleotides and amino acids alignment, choice of amplification primers, analysis of protein structures.

Teaching

Lectures and computer exercises 

Innovative teaching methods

Problem-based learning.

Learning by doing

Attendance

no

Course books

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), in which a large part of the course topics will be addressed from a practical point of view using bioinformatics tools

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.

Teaching

slides and exercises on blended platform. Non-attending students are strongly encouraged to contact the professor

Attendance

no

Course books

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.