Learning objectives
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The course aims to provide the student with the basic tools for using the information on the sequence and structure of biological macromolecules. The student will learn the theory and practice of using the most common sequence analysis software programs.
Prerequisites
Basic knowledge of biological macromolecules. <br />
Basic practice in the use of the computer and Internet
Course unit content
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Introduction to bioinformatics: meaning and fields of bioinformatics. Bioinformatics topics: DNA and protein sequences, DNA and protein structures. Evolution of biological information over time. <br />
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. <br />
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. <br />
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. <br />
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 <br />
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
Introduzione alla bioinformatica A. M. Lesk, McGraw-Hill, 2003 <br />
Bioinformatica A. Tramontano, Zanichelli 2002
Teaching methods
Teaching method: <br />
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The course is divided into theoretical lectures and practical exercises. In the practical exercises, the students tackle a sequence analysis problem using a computer. <br />
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Assessment method: <br />
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Written test consisting of: a) a practical part in which the student must show that he/she is able to solve a sequence analysis problem using a computer; b) a theoretical part with multiple-choice questions. A short oral exam follows the written test.
Assessment methods and criteria
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Other information
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