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Introduction to Marine Genomics pp 315–378Cite as

Practical Guide: Genomic Techniques and How to Apply Them to Marine Questions

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Part of the book series: Advances in Marine Genomics ((AMGE,volume 1))

Abstract

In recent years, modern high-throughput techniques in genome and post-genome research have made a marked impact on the marine sciences. Today, massively parallel DNA sequencing and hybridization approaches allow the identification of not only the gene repertoire but also the gene regulatory networks that function within an organism. The huge amounts of data acquired from such experiments can only be handled with intensive bioinformatics support that has to provide an adequate infrastructure for storing and analysing these data. Bioinformatics has to deliver efficient data analysis algorithms, user-friendly tools and software applications, as well as extensive hardware infrastructure to deal with these genome-scale analyses.

The following chapter briefly introduces not only the most relevant topics of bioinformatics for functional and structural genomics but also addresses the practical aspects of other steps of a genome project such as sequencing or data management issues. The chapter will take the reader through the different technical approaches that can be applied in marine genomics projects.

In the first part, we will mainly focus on data generation, introducing classical genome sequencing approaches such as the Sanger method and the shotgun technique. Moreover, a short overview of the current status of the next generation of sequencing techniques will be given. In the second part, we briefly introduce the concept of data management for bioinformatics applications. In the third part, we describe the basic principles of genome sequence analysis and address topics like EST clustering and genome assembly, gene prediction, gene function assignment and classification as well as whole genome annotation. In the fourth part of this chapter, we present an overview of transcriptome data analysis using microarray hybridization technology. After a brief introduction to microarray technology we describe state-of-the-art methods for image processing, data normalization, significance testing and cluster analysis.

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Notes

  1. 1.

    Usually frequencies of oligonucleotides of length between 3 and 12 bp are modelled.

  2. 2.

    Specificity measures the reliability of the predictions. It is defined as the fraction of correct gene predictions, i.e. the fraction of predicted genes that corresponds to known genes.

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Acknowledgments

We are grateful to the CeBiTec at Bielefeld University, the BMBF Competence Network GenoMik-Plus (grant 0313805A), the International NRW Graduate School in Bioinformatics and Genome Research, the EU FP6 Network of Excellence Marine Genomics Europe (contract No. COGE-CT-2004-505403) and Nestlé Research Center for financial support of our work. Special thanks to our native speaker Sita Lange, the chapter would not have been the same without her efforts. The authors would also like to thank Guy Cochrane, Naryttza Diaz, Michele Magrane, Nicky Mulder, Kai Runte and Rafael Szczepanowski, who read sections of the chapter and provided valuable comments. Many thanks to our present and former colleagues from the Junior Group Computational Genomics for their patience during the writing.

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Authors and Affiliations

  1. BRF/Computational Genomics group, CeBiTec, Universität Bielefeld, D33594, Bielefeld, Germany

    Virginie Mittard-Runte, Thomas Bekel, Jochen Blom, Kolja Henckel, Sebastian Jaenicke, Burkhard Linke, Heiko Neuweger & Alexander Goesmann

  2. International NRW graduate school in Bioinformatics and Genome Research, CeBiTec, Universität Bielefeld, D33594, Bielefeld, Germany

    Susanne Schneiker-Bekel

  3. BioAnalytical Science Department, Nestlé Research Center, CH-1000, Lausanne 26, Switzerland

    Lutz Krause

  4. Computational Biology Unit, Unit BCCS, Thormøhlensgate 55, N-5008, Bergen, Norway

    Michael Dondrup

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Correspondence to Virginie Mittard-Runte .

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Editors and Affiliations

  1. CNRS UMR 7139, Labo. Végétaux Marins et Biomolécules, Université Paris VI, place Georges Teissier, Roscoff CX, 29682, France

    J. Mark Cock

  2. Max F. Perutz Laboratories GmbH, Dr. Bohr-gasse 9/4, Wien, 1030, Austria

    Kristin Tessmar-Raible

  3. CNRS UMR 7139, Labo. Végétaux Marins et Biomolécules, Université Paris VI, place Georges Teissier, Roscoff CX, 29682, France

    Catherine Boyen

  4. Equipe Diversité et Connectivité dans le, Paysage Marin Côtier (DIV&CO), Université Paris VI, place Georges Teissier, Roscoff CX, 29682, France

    Frédérique Viard

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Mittard-Runte, V. et al. (2010). Practical Guide: Genomic Techniques and How to Apply Them to Marine Questions. In: Cock, J., Tessmar-Raible, K., Boyen, C., Viard, F. (eds) Introduction to Marine Genomics. Advances in Marine Genomics, vol 1. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-8639-6_9

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