Bioinformatics

Code

11011

Academic unit

Faculdade de Ciências e Tecnologia

Department

Departamento de Ciências da Vida

Credits

6.0

Teacher in charge

João Manuel Gonçalves Couceiro Feio de Almeida

Weekly hours

4

Total hours

58

Teaching language

Português

Objectives

The main goal is to present an introductory panorama of the bioinformatics tools available today and their rational utilization.

The students will acquire knowledge and proficiency on current tolls for several basic goals: sequence internal and comparative analysis; database search; and content visualization.

All the tools presented during the course are freely accessible through user interfaces in the World Wide Web.

Basic concepts from the fields of informatics (hardware, software, and networking), and bioinformatics (information, notation, annotation, alignment, similarity, public databases, search engines, electronic benches, and algorithms) are either taught or revisited.

Student informatics skills are leveled before introducing more sophisticated topics. Most topics are to be object of hands-on lab sessions.

Prerequisites

The students must understand the basic concepts on molecular biology and have knowledge on the related techniques. Prior knowledge on biology and biochemistry are needed.

 

The students should have some acquaintance with PC-type computers running a Microsoft Windows environment.

 The students should have an intermediate command of English since most of the presented content is written in this language.

Subject matter

Bioinformatics as a toolbox to address modern Biology questions.

Informatics systems as the tools of the trade.

Biological sequences as a registry of information contained in biomolecules.

The ways, and means to effectively store/retrieve sequence data.

Algorithms to extract information from a sequence, and their respective implementations.

Sequence alignments, similarity, and homology.

Substitution matrices.

Inference about structure, and function for amino acid sequences.

Algorithms for fast sequence matching, and sequence database querying.

The main public databases for biological research (PubMed, INSDC, UniProt).

Bibliography

Pevsner, Jonathan. Bioinformatics and Functional Genomics. 2nd ed. Wiley-Blackwell, 2009.

Lesk A. Introduction to Bioinformatics (2nd Ed.).Oxford University Press, 2005, Oxford. (ISBN 0 19 927787 7)

Orengo C., Jones D., Thornton J. Bioinformatics: Genes, Proteins and Computers. Advanced Text. BIOS Scientific Publishers Limited, 2003, Oxford. (ISBN 1 85996 054 5)

Claverie J.-M., Notredame, C. Bioinformatics for Dummies. Advanced Text. For Dummies, 2003, ?. (ISBN 0 76451 696 5)

Bergeron B. Bioinformatics Computing. PTR, Prentice Hall, 2003, New Jersey. (ISBN 0 13 100825 0)

Web content available through selected hyperlinks.

Teaching method

The main concepts are presented in lectures. Presentation and source material are made available to the students through the WWW.Hands-on sessions where students follow a given protocol and are faced a final self-evaluation test.

Evaluation method

Assessment Items

• Weekly mini tests (group submission) - >=11 pcs
• 30 %
• student groups may exchange two (2) of these tests for a written report.
• Individual Test - 1 pcs
• 30 %
• Other aspects
• Spoken participation – 5 %
• Self-assessment check – 5 %
• Balancing peronal vs. group performance – 30%
• avg(individualTest,avg(miniTest))-(avg(miniTest)-individualTest)
• Final Exam – 95 % (+ 5 %, self-assessment check)

Eligibility for Assessment

• In accordance with the current school rules.

Diagnostic Testing

• Student background knowledge will be assessed in order to determine their chance of success in this course.

Courses

• Cell and Molecular Biology