PRINCIPI DI BIOINFORMATICA A - L

Module PRINCIPI DI BIOINFORMATICA

The aim of this course is to build an introductive theoretical knowledge of the Bioinformatic softwares, of their features and limitations and to give to the students the ability to utilize the most popular tools available on the web.

In addition, during the course, learners will be provided with the elements of programming in Python and R.
Python and R are very powerful programming languages and represent an excellent trade-off between simplicity and efficiency.
Students will acquire the ability to use, modify and develop applications written with a high-level programming language, aimed at applications in the bioinformatics field.
In particular, the course aims to provide students with:
    - Basic knowledge of high-level programming languages
    - Ability to develop simple programs according to the imperative and object oriented programming paradigm
    - Ability to modify and apply existing programs and software libraries in new contexts
    - Ability to use software libraries for problems relevant to bioinformatics

The lectures will consist of PowerPoint presentations. There will also be online exercises and demonstrations with the most popular bioinformatics websites. In the exercises, students will be asked to perform simple exercises on the topics covered.

The exam will consist of an oral interview supplemented with written exercises

Information for students with disabilities and/or DSA
In order to guarantee equal opportunities and in compliance with the laws in force, interested students can ask for a personal interview so that any compensatory and/or dispensatory measures can be planned, based on the teaching objectives and specific needs. They can also contact the CInAP (Centro per l'integrazione attivo e Partecipata - Servizi per le Disabilità e/o i DSA) contact person in the Department of Biomedical and Biotechnological Sciences.

* Introduction to high-level programming languages, with special reference to bioinformatics
* Algorithms, flow charts
* Programming paradigms: imperative and object oriented
* Python and R: introduction and basic concepts
* Use of libraries in R and Python for bioinformatics

Medline and the most popular websites and bibliographic databases for bibliographic information in Biology
Biological databases: nucleic acid and protein databases, specialized databases – new data submission – retrieval of sequences databases
Sequence alignment – computing the alignment of two sequences – significance of alignments – FASTA and BLAST, alignment programs for screening sequence databases
Multiple sequence alignment – Clustal W
Search for motifs and conserved structures by comparative analysis
Phylogeny – phylogenetic trees – molecular clock

Stefano Pascarella, Alessandro Paiardini.  Bioinformatica  Dalla sequenza alla struttura delle proteine.  Zanichelli 2011

Manuela Helmer Citterich, Fabrizio Ferrè, Giulio Pavesi, Graziano Pesole, Chiara Romualdi.  Fondamenti di bioinformatica.  Zanichelli  2018