Chapter 9
Practical Guide: Genomic Techniques and How
to Apply Them to Marine Questions
Virginie Mittard-Runte, Thomas Bekel, Jochen Blom, Michael Dondrup,
Kolja Henckel, Sebastian Jaenicke, Lutz Krause, Burkhard Linke,
Heiko Neuweger, Susanne Schneiker-Bekel, and Alexander Goesmann
Abstract In recent years, modern high-throughput techniques in genome and postgenome 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.
V. Mittard-Runte (B)
BRF/Computational Genomics group, CeBiTec, Universität Bielefeld,
D33594 Bielefeld, Germany
e-mail: vrunte@cebitec.uni-bielefeld.de
315
J.M. Cock et al. (eds.), Introduction to Marine Genomics,
Advances in Marine Genomics 1, DOI 10.1007/978-90-481-8639-6_9,
C
Springer Science+Business Media B.V. 2010
Practical Guide: Genomic Techniques and How
to Apply Them to Marine Questions
Virginie Mittard-Runte, Thomas Bekel, Jochen Blom, Michael Dondrup,
Kolja Henckel, Sebastian Jaenicke, Lutz Krause, Burkhard Linke,
Heiko Neuweger, Susanne Schneiker-Bekel, and Alexander Goesmann
Abstract In recent years, modern high-throughput techniques in genome and postgenome 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.
V. Mittard-Runte (B)
BRF/Computational Genomics group, CeBiTec, Universität Bielefeld,
D33594 Bielefeld, Germany
e-mail: vrunte@cebitec.uni-bielefeld.de
315
J.M. Cock et al. (eds.), Introduction to Marine Genomics,
Advances in Marine Genomics 1, DOI 10.1007/978-90-481-8639-6_9,
C
Springer Science+Business Media B.V. 2010