Introduction to the course, principal types of file. Multiple sequence alignment. BLAST (Basic Alignment Search Tool). Bases of molecular evolution. Phylogeny (methods and application). Methods for the identification of Horizontal Gene Transfer and bacteria identification. Analysis of 3D structure of proteins. Analyses of expression data and functional assignment. Genomics. Algorithms in Bioinformatics. Metabolic modelling.
Scientific peer rewiew papers discussed during classes
Learning Objectives
Knowledge acquired:
Main bioinformatics techniques and approaches for the study of biological problems. Web resources and their use. Massive sequencing of genomes and post-processing of data. Molecular evolution (basics). Metabolism and metabolic networks. Metabolic modeling (basics).
Competence acquired
Sequence retrieval in public databases. Sequence similarity searches in public databases. Multiple sequence alignment. Phylogenetic tree construction and interpretation. Genome annotation. Metabolic pathways analysis.
Skills acquired (at the end of the course):
Workflow: from genic sequence to phylogenetic tree construction; use of innovative bioinformatics and computational techniques to characterize de novo sequenced genomes in both evolutionary study than applicatory such as metabolic engineering;
.
Teaching Methods
Total hours of the course (including the time spent in attending lectures, seminars, private study, examinations, etc...): 48
Hours reserved to private study and other indivual formative activities:
Contact hours for: Lectures (hours): 28
Contact hours for: Laboratory (hours): 20
Contact hours for: Laboratory-field/practice (hours):
Seminars (hours): 0
Stages: 0
Intermediate examinations: 0
Further information
Frequency of lectures, practice and lab:
Highly recommended.
Teaching tools
Informatics classroom
Office hours:
By appointment
renato.fani@unifi.it
(+39) 055 4574742
Type of Assessment
Exam modality:
Written and practical test
Course program
Introduction to the course and main web bioinformatics resources (NCBI, KEGG, MetaCyc, InterPro). Main types of files in bioinformatics (FASTA, SBML, PDB). Sequence retrieval and multiple sequence alignment (BioEdit Package). Sequences editing and identification of conserved motifs in biological sequences. Study case: RND efflux system. The homology-based sequence search tool BLAST (Basic Alignment Search Tool). Fundamentals of molecular evolution and phylogenetic tree construction (methods and applications). Mega5 package for molecular evolution analyses. Study cases: horizontal gene transfer and bacterial identification. Analysis of 3D structure conservation of proteins. Analysis of gene expression data and functional annotation of sequences. Genomics and analysis of massive sequencing data. Assembly, Annotation and comparative Analysis of sequences. Main algorithms in bioinformatics. Simulation of a typical bioinformatics pipeline. Metabolic network reconstruction of a cell. Techniques for metabolic modelling