Genomics and bioinformatics [SMMMM116]

Learning outcomes

At the end of the course, the student will be able to perform protein sequence analyses, protein structure prediction and understand the bases of phylogenetic reconstruction.

The student will be capabe of performing some genomic analyses, like assembly, mapping to reference genomes, variant calling and comparative analyses. 

Objectives

To give the basic principles of bioinformatics methods for the analyses of proteins and genomes and to discuss the power and limits of bioinformatics.

To apply bioinformatics methods to identify genes/proteins, predict their functions, establish evolutionary relationships and predict protein structure and protein complexes, comparative genomics and -omics integration tools.

Content

The course is divided in modules:

1. Protein sequence analyses, phylogeny, protein structure prediction, databases

2. Genomics.

Table of contents

Protein module

• Database search
• Sequence alignment (pairwise)
• Multiple Sequence alignment 
• Gene ontology
• Protein structure prediction with AlphaFold2 and structural alignment.
• Phylogeny

Module Genomes Genome annotation

• Genome assembly / annotation
• Comparative genomics
• Metagenomics

Exercises description

Bioinformatics -based projects.