4 Computational Tools and Resources in Plant Genome Informatics

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Computational Tools and Resources


in Plant Genome Informatics
Todd J. Vision1 and Aoife McLysaght2
1
Department of Biology, University of North Carolina at Chapel Hill,Chapel Hill, NC, USA,
and 2 Ecology and Evolutionary Biology, University of California, Irvine, CA, USA

INTRODUCTION greatly. The resources we describe range drastically


in sophistication from little tested programs posted
Though all biologists deal with information, only on graduate student web pages to very stable and
recently have the computational challenges of complex databases maintained by governmental
systematically collecting, storing, organising, man- agencies. The better ones typically provide manuals
ipulating visualising and analysing large amounts and tutorials, often containing descriptions of
of biological information come to be widely the underlying principles. The reader is strongly
appreciated. The cause of this is the explosive advised to consult the documentation available for
growth of genomics. The term bioinformatics was each tool.
originally coined for the application of information Though a wide array of commercial resources
technology to large volumes of biological, and par- exist, some of which are ideally suited to specific
ticularly genomic, data. The field of bioinformatics tasks, many of the most fundamental and long-
has come to be intermingled with traditional lived bioinformatics tools are freely available. For
computational biology and biostatistics, which this reason, we describe primarily non-commercial
are strictly concerned not with how to handle software in this chapter. Many of the databases
the information itself, but rather how to extract and analysis tools we describe are hosted by
biological meaning from it. Thus, bioinformatics, government or academic research centres and
in its broad sense, can be seen as providing both can be accessed via user-friendly web interfaces.
the infrastructure and the scientific framework Tables 4.1 and 4.2 list the Uniform Resource
in which biologists take information and use Locators (URLs) for all the online resources that
computers to help convert it into knowledge. are discussed in the text.
Despite the relative youth of the field as a
recognised discipline, there is an impressive diver-
sity of bioinformatics resources currently available. WHAT IS OUT THERE AND HOW TO GET IT
By necessity, we only focus on a small slice of
this diversity here. We pay particular attention Collectively, online databases allow access to a
to sequence analysis because of its centrality to staggering quantity of data. This partly reflects
genomics. We also do not attempt to provide the way much biological data is now collected.
specific protocols, as the specific needs of users vary Genome projects popularised the concept of

Handbook of Plant Biotechnology


Edited by Paul Christou and Harry Klee 
C 2003 John Wiley & Sons Ltd

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