Studying at the University of Verona
Here you can find information on the organisational aspects of the Programme, lecture timetables, learning activities and useful contact details for your time at the University, from enrolment to graduation.
Study Plan
This information is intended exclusively for students already enrolled in this course.If you are a new student interested in enrolling, you can find information about the course of study on the course page:
Laurea in Bioinformatica - Enrollment from 2025/2026The Study Plan includes all modules, teaching and learning activities that each student will need to undertake during their time at the University.
Please select your Study Plan based on your enrollment year.
1° Year
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2° Year activated in the A.Y. 2015/2016
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3° Year activated in the A.Y. 2016/2017
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Un insegnamento a sceltaDue insegnamenti a scelta| Modules | Credits | TAF | SSD |
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Un insegnamento a sceltaDue insegnamenti a sceltaLegend | Type of training activity (TTA)
TAF (Type of Educational Activity) All courses and activities are classified into different types of educational activities, indicated by a letter.
Biochemistry (2015/2016)
Teaching code
4S00103
Credits
12
Coordinator
Language
Italian
Also offered in courses:
- Bioinformatics and biological databases of the course Bachelor's degree in Biotechnology
The teaching is organized as follows:
Learning outcomes
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MM: ELEMENTI DI BIOCHIMICA
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MM: LABORATORIO DI BIOINFORMATICA I
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The course will provide the theoretical and practical basis to understand and employ algorithms and programs currently used in Bioinformatics. Major biological databases will be introduced with a special focus on genomic, proteomic and biochemical information. The students will also be introduced to the most modern fields of structural bioinformatics and systems biology.
Program
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MM: ELEMENTI DI BIOCHIMICA
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MM: LABORATORIO DI BIOINFORMATICA I
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Theoretical Module - Overview of the main structural features of proteins and nucleic acids in relation to the concept of evolution. Introduction to biomolecular databases: online resources and their use - Biological databases: organization and integration of information concerning: a) protein and nucleic acid sequences; b) biomolecular structures; c) bibliographic and scientific literature. Retrieve of specific information: use of limitations and Boolean operators. - Sequence comparison and alignments: static and dynamic algorithms; substitution matrices (PAM,BLOSUM) - - Search-algorithms: FASTA and BLAST; Smith-Waterman; Needleman-Wunsch; statistic significance for an alignment (z-score, expectation values and probability) - Multiple sequence alignments: ClustalW, search on specific databases, other algorithms, PSI-BLAST - Short introduction on philogenetic trees - Introduction to Structural Bioinformatics: visualization and analysis of protein and nucleic acid 3D structures - Methods to predict protein secondary structure elements starting from the sequence - Introduction to Systems Biology: Spatial and temporal scales, static and dynamic models, mathematical frameworks, introduction on signal transduction networks Laboratory Module - Introduction to Linux - NCBI databases: Entrez interface, Gene, UniGene, Protein, Uniprot and EBI - Single and multiple sequence alignments, score matrices, optimal methods; online resources and spreadsheets - BLAST,PSI-BLAST and BLAT: online tools and their use - Tools for multiple alignments, the Homologene databank, computation and visualization of multiple alignments - Tools for phylogenesis : Mobyle (Institut Pasteur and Phylogeny.fr) - Introduction to PyMol and molecular visualization. Use of PSI-PRED and JPRED for predicting secondary structures from sequences - Systems biology: numerical simulation of simple biochemical reactions. Building simple kinetic models by using SBOTOOLBOX2 for Matlab; application to G-potein signalling cycles.
Bibliography
| Author | Title | Publishing house | Year | ISBN | Notes |
|---|---|---|---|---|---|
| BERG-TYMOCZKO- STRYER | BIOCHIMICA (Edizione 7) | ZANICHELLI | 2012 |
Examination Methods
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MM: ELEMENTI DI BIOCHIMICA
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MM: LABORATORIO DI BIOINFORMATICA I
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Written exam for both modules. The two marks will be averaged. Students can chose to prepare a presentation in groups of 3-4 students on a selected database, which will also contribute to the final mark. An oral examination can be chose in addition, in order to improve the final mark.
