First cycle
degree courses
Second cycle
degree courses
Single cycle
degree courses
School of Science
BIOTECHNOLOGY
Course unit
INFORMATICS AND BIOINFORMATICS PRACTICAL
SCP3058337, A.A. 2017/18

Information concerning the students who enrolled in A.Y. 2015/16

Information on the course unit
Degree course First cycle degree in
BIOTECHNOLOGY
IF1839, Degree course structure A.Y. 2011/12, A.Y. 2017/18
N0
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Number of ECTS credits allocated 7.0
Type of assessment Mark
Course unit English denomination INFORMATICS AND BIOINFORMATICS PRACTICAL
Website of the academic structure http://biotecnologie.scienze.unipd.it/2017/laurea
Department of reference Department of Biology
Mandatory attendance
Language of instruction Italian
Branch PADOVA
Single Course unit The Course unit can be attended under the option Single Course unit attendance
Optional Course unit The Course unit can be chosen as Optional Course unit

Lecturers
Teacher in charge FRANCESCO FILIPPINI BIO/11

Mutuated
Course unit code Course unit name Teacher in charge Degree course code
SCP3056703 OTHER ACTIVITIES ON INFORMATION AND COMMUNICATION SUBJECT FRANCESCO FILIPPINI IF1839

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Educational activities in elective or integrative disciplines BIO/11 Molecular Biology 5.0
Other -- -- 2.0

Course unit organization
Period Second semester
Year 3rd Year
Teaching method frontal

Type of hours Credits Teaching
hours
Hours of
Individual study
Shifts
Practice 2.0 32 18.0 No turn
Laboratory 0.5 8 4.5 No turn
Lecture 4.5 36 76.5 No turn

Calendar
Start of activities 26/02/2018
End of activities 01/06/2018

Examination board
Board From To Members of the board
4 INFORMATICA E BIOINFORMATICA 2018-2019 01/10/2018 30/11/2019 FILIPPINI FRANCESCO (Presidente)
BERGANTINO ELISABETTA (Membro Effettivo)
ROMUALDI CHIARA (Supplente)
3 INFORMATICA E BIOINFORMATICA 2017/2018 01/10/2017 25/11/2018 FILIPPINI FRANCESCO (Presidente)
BERGANTINO ELISABETTA (Membro Effettivo)
ROMUALDI CHIARA (Supplente)
2 INFORMATICA E BIOINFORMATICA 2016-2017 01/10/2016 30/11/2017 FILIPPINI FRANCESCO (Presidente)
BERGANTINO ELISABETTA (Membro Effettivo)
ROMUALDI CHIARA (Supplente)

Syllabus
Prerequisites: Basic knowledge in Molecular Biology and Biochemistry (DNA, RNA, proteins, gene structure and function, transcriptional regulation, proteins, protein domains and sites, cloning and expression, DNA sequencing).
Target skills and knowledge: Students are expected to acquire metodological and scientific knowledge and practical abilities concerning the course topics (as reported in section "Contenuti").
Examination methods: Concerning the Informatics part of the course, students will demonstrate their own practical abilities by contributing a scientific report on the test activity in the PC classroom, consisting of the integration between information that can be retrieved from bibliographic, sequence and signature databases (e.g. PubMed literature, functional annotation from UniProt/Genbank/InterPro etc. entries) and information that can be inferred from sequence or structural similarity; assessment of theoretical knowledge is based on questions on course topics and/or presentation of scientific articles reporting on in silico research.
Concerning the Bioinformatics part of the course, the exam is based on multiple reports on practical activities and an interview on both practice and theorectical knowledge.
Assessment criteria: The evaluation process is based on the main criterium that students should properly combine theoretical knowledge and practical, problem solving capacity.
Therefore, in addition to questions on algorithms, the exam will also consist of the evaluation of practical capacities when using analysis/prediction tools.
Course unit contents: PART OF INFORMATICS:
Lesson topics:
- Informatics basics on hardware and software architecture. Operating Systems, programs and programming languages. Internet and communication protocols.
- Biomedical and bioinformatic databases in the context of Biotechnologies. Bio-data management. Crucial elements in databases: structural order, entries/records, fields and levels. Cross-refs in databases. Main international databases and bioinformatic organizations. Simple and advanced queries, boolean combinations, NCBI and EBI search tools.
- Sequence analysis basics on BLAST and functional markers
Practice:
- simple and advanced queries in databases
- simple sequence analysis based on homology, structural similarity or shared motifs

PART OF BIOINFORMATICS:
The Bioinformatics in the context of Biotechnology and Molecular Biology. Alignment of DNA and protein sequences: potential, limits and correct analysis of results. Similarity evaluation criteria. Globale and local alignment. Scoring systems. Matrices: "dot plot", PAM and BLOSUM. The BLAST algorithm and its basic and special applications. How to select a method based and how to interpretate results. Search tuning by settings modification and search iterations. Filters and output options. Multiple alignment as a tool for identifyinc consensus sequences. Sequence tags in protein sequences: regular expressions and profiles. Repeat regions: biological relevance of frequence and spreading. Pattern scanning in proteins. PROSITE. Precisione and recall indexes. Secondary structure prediction. Structural databases and entries: PDB. Structure-based alignments and sequence tags. Promoters patterns in DNA sequences and identification of regulatory regions. Regulatory networks and co-regulation. miRNA and miRNA target prediction. Examples of reasearch articles reporting on computer-aided biotechnology.
Practical activities focus on using main publicly available tools for similarity search (BLAST family applications), regular expression and profile scanning (ScanProsite, PROscan) and on their integration as analysis and prediction tools.
Planned learning activities and teaching methods: Learning will take advantage from lessons, interaction among the teacher and the students, as well as from available didactic material.
Part on Informatics is based on both lessons and practical data mining and simple sequence analysis in the computer classroom.
The Bioinformatics part will be also based on interactive lessons and on "problem solving" activities at the PC, consisting in training exercises followed by a test with report. Pre-exam training will also occur, including examples of questions and how to properly formulate responses.
Additional notes about suggested reading: Resources for the students are located at a web site created for the course and updated every year. Such a website contains - as free download pdf files - the complete material concerning lessons and theoretical knowledge, as well as the online guide to all practical activities, the course schedule, links to remote resources, eventual warning messages.
Textbooks (and optional supplementary readings)