Bioinformatics for plant genome annotation

Large amounts of genome sequence data are available and much more will become available in the near future. A DNA sequence alone has, however, limited use. Genome annotation is required to assign biological interpretation to the DNA sequence. This thesis describes a variety of research topics for bioinformatics in the context of genome annotation. A review of the various topics and issues in the science of genome annotation is given in Chapter 2. The next chapter (3) describes the development of a system for automated, high throughput, genome annotation called Cyrille2. Chapter 4 focuses on interactive and intuitive visualization of different types of annotation data. Chapter 5 describes a new approach for the prediction of potential micro-RNAs (miRNAs) in a plant genome. Chapter 6 of this thesis focuses on proteins and the prediction of a particular protein feature, allergenicity.The overall scope of this thesis is broad and many of the challenges for bioinformatics in genome annotation are encountered. The primary challenges are reviewed in the final discussion of this thesis (Chapter 7) and concludes that these challenges fall into two main categories: communication and quality. Communication in bioinformatics for genome annotation is a major challenge on multiple levels; between computers, between humans and inbetween computers and humans. Each level brings its own challenges and requires different solutions. The quality of annotation data is the second major issue. Most annotations depend on previous annotations. The quality of these predictions obviously rely on the quality of the underlying data and are therefore susceptible to error propagation. A quality indication system that covers the data behind an annotation seems essential for the future of genome annotation.Current technological developments indicate dramatic increases in data production speed for genomics and related areas. Combined with the knowledge that only a small percentage of any genome is understood ensures that genome annotation will remain one of the more exciting and challenging fields of bioinformatics for decades to come.

Bibliographic Details

Main Author:	Fiers, M.W.E.J.
Other Authors:	Stiekema, W.
Format:	Doctoral thesis biblioteca
Language:	English
Subjects:	bioinformatics, computer analysis, dna sequencing, genome analysis, genomes, genomics, plants, bio-informatica, computeranalyse, dna-sequencing, genexpressieanalyse, genomen, genoomanalyse, planten,
Online Access:	https://research.wur.nl/en/publications/bioinformatics-for-plant-genome-annotation
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