First cycle
degree courses
Second cycle
degree courses
Single cycle
degree courses
School of Science
EVOLUTIONARY BIOLOGY
Course unit
BIOINFORMATIC 2
SC06100858, A.A. 2017/18

Information concerning the students who enrolled in A.Y. 2017/18

Information on the course unit
Degree course Second cycle degree in
EVOLUTIONARY BIOLOGY
SC1179, Degree course structure A.Y. 2009/10, A.Y. 2017/18
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Number of ECTS credits allocated 6.0
Type of assessment Mark
Course unit English denomination BIOINFORMATIC 2
Website of the academic structure http://biologia.scienze.unipd.it/2017/laurea_magistrale_biologiaevoluzionistica
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 STEFANIA BORTOLUZZI BIO/13

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Other -- -- 4.0
Core courses BIO/11 Molecular Biology 2.0

Mode of delivery (when and how)
Period First semester
Year 1st Year
Teaching method frontal

Organisation of didactics
Type of hours Credits Hours of
teaching
Hours of
Individual study
Shifts
Practice 1.0 16 9.0 No turn
Laboratory 1.0 16 9.0 No turn
Lecture 4.0 32 68.0 No turn

Calendar
Start of activities 02/10/2017
End of activities 19/01/2018

Syllabus
Prerequisites: Basic knowledge of genetics and molecular biology will help in the understanding of the biological motivations of bioinformatics. Basic skills in computer science.
Target skills and knowledge: The course will give medium-advanced skills in all the classic topics of bioinformatics, covering databases and data retrieval, sequence alignments and similarity searches, structure predictions, and NGS applications to genomics and transcriptomics.
Examination methods: Written test.
Evaluation of 8 practical sessions.
The Journal Club will be also evaluated.
Assessment criteria: In their final examination the students should demonstrate a systematic understanding of the field and mastery of the methods of research associated with it, integrating the subjects of this course with other knowledge.
Course unit contents: Database e data retrieval.
Algorithms for pairwise alignments, substitution matrices.
Similarity searches.
Multiple alignments: progressive (Clustal Omega) and consistency-based (Tcoffee) methods.
Biomolecule structure prediction: secondary structure prediction and protein folding (ab inizio, comparative modeling, threading).
Genomics resources (NCBI, UCSC Genome Browser, ENSEMBL).
Genome sequencing, assembly, and annotation; Genome resequencing.
Introduction to RNA-seq data analysis.
Comparative genomics.
Practical sessions using Shell and Python programming.
Planned learning activities and teaching methods: The course will include lectures and practicals.
Journal Club (Bioinformatics applied in Comparative Genomics and Molecular Evolution).
Additional notes about suggested reading: - Recommended Book: Bioinformatica. Dalla sequenza alla struttura delle proteine. Stefano Pascarella, Alessandro Paiardini. Zanichelli. 2014

- Lecture notes and other teaching material: http://compgen.bio.unipd.it/~stefania/Didattica/

- More info regarding the study of specific topics will be distributed in the course.
Textbooks (and optional supplementary readings)