Learning objectives
Practical notions of searches in biological databases and sequence analysis
Prerequisites
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Course unit content
Introduction to bioinformatics: meaning and fields of bioinformatics. Bioinformatics topics: DNA and protein sequences, DNA and protein structures. Evolution of biological information over time.
Databases of biological sequences: definition and purpose of databases; main DNA (GenBank, DDBJ, EMBL) and protein (SwissProt, Pir) databases. Interrogation and consultation of databases. Syntax of the FASTA format for sequences.
Comparison of sequences: meaning and purpose of sequence alignment; pairwise alignment. Local and global alignment algorithms. Gap creation penalty and gap extension penalty. Amino acid substitution matrices. Use of Needle and Water programs.
Search for homology: meaning of homology. Alignment significance measurements. Programs for homology searches in databases. Use of the Blast program and reading of the homology search result.
Multiple alignment and phylogenesis: uses of multiple alignment. Use of the ClustalX program. Displaying multiple alignment. Use of the GeneDoc program. Phylogenetic reconstruction with the neighbour-joining algorithm implemented in Clustal. Displaying phylogenetic trees with the Treeview program
Prediction of the biochemical characteristics of proteins: chemico-physical characteristics of proteins. Use of the ProtParam program. Prediction of the cellular location of proteins. Use of the PSort and SignalP programs. Structure of proteins. Consultation of the PDB structure database. Displaying the structures with the Rasmol program
Full programme
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Bibliography
A. Tramontano - Bioinformatica, Zanichelli 2002
Teaching methods
Lectures, practical exercise in a computer room
Assessment methods and criteria
Solution of bioinformatics problems during exercises in the classroom. Written test of bioinformatic analysis.
Final oral exam
Other information
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