Genomics, transcriptomics and proteomics

Semester 1

Semester 2

Semester 3

Semester 4

ECTS
6

PRODUCTION
ENVIRONMENT

Biotechnology
University of Algarve

Synopsis

This discipline explores the concept of omics and the application and challenges of the technology. Datasets coming from experiments will be analysed to give students hands-on training so they can handle, analyse and critically interpret omics data. A theoretical introduction is given to the three modules and then students work with the datasets available.

Content

The discipline will explore the basic principals in genomics, transcriptomics and proteomics. Interpretation and understanding data coming from "omics" will involve the application of bioinformatics tools. The discipline will start with a biochemistry and molecular biology refresher about basic concepts of biochemistry of nucleic acids and proteins. This will be followed by a refresher about cell biology in relation to genome, transcription and translation to set the scene for understanding and interpreting "omics" data. The main technologies and approaches will be outlined in relation to DNA, RNA and proteins and then their application to resolve real-life experimental question will be outlined.
The theoretical-practical component of the discipline will involve handling genomics, transcriptomics and proteomics datasets using available software followed by analysis of the results and critical discussion of the approach and data interpretation.

Pre-requisites

BSc in science. Basic bioinformatics.

Aims

To learn the importance of genomics, transcriptomics and proteomics for understanding organisms to ecosystem function. To reveal the key approaches in omics and their use in Marine science. To illustrate the strengths, opportunities and limitations of omics technologies. Extracting socioeconomics benefits from Marine "omics".

Objectives

Students will become conversant with the main technologies available for generation of genomics, transcriptomics and proteomics data. Development of hands-on skills in relation to handling genomics data (eg. gene annotation, alignments) phylogenetic trees and synteny analysis), transcriptomics data (eg. gene expression analysis and techniques, gene ontology, Blast2Go, String analysis, primer design etc) and proteomics (eg. characterization of proteins, interpretation of MALDI-TOF results, Mascot and related programs). At the end of the module students will be able to design and implement procedures for handling data coming from omics.

Key skills acquired

1) Knowledge and understanding of technologies and applications of omics.
2) The use of omics to answer questions in marine biology and related fields.
3) The ability to design and implement a strategy to handle "big data" sets.
4) Analyse and interpret data coming from genomics, transcriptomics and proteomics.
5) Presentation of data coming from genomics, transcriptomics and proteomics.

Bibliography

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Research, 2007, Vol. 35.
The Ensembl genome Database Project. Nucleic Acids Research, 2002, Vol. 30, No. 1
A vision for the future of genomics research: A blueprint for the genomic era. NATURE, 2003. Vol 422, 24
D. W. Mount (2004) Bioinformatics: Sequence and Genome analysis 2nd Ed, Cold Spring Harbour Laboratory Press
D. Higgins and W. Taylor (2001) Bioinformatics: sequence, structure and databanks -a practical approach, Oxford University Press
NCBI (http//:www.ncbi.nlm.nih.gov/About/outreach/courses.html)
Swiss-Prot (http://www.expasy.org/sprot/sp-docu.html)

Assessment

Each module, genomics, transcriptomics and proteomics will be individually evaluated through; 1) an exam and 2) completion of practical assignments given during each module and group discussion.

Involved teachers

Joao Cardoso (jccardo@ualg.pt) Patricia Pinto (ppinto@ualg.pt) Liliana Anjos (lanjos@ualg.pt)

Contact hours

lectures
9

practicals
0

seminars
2

computerclass
24

fieldwork
0

other
0