This document summarizes some of the computational tools and resources available for plant genome informatics. It introduces how bioinformatics has grown to help biologists analyze and extract meaning from large amounts of biological data, particularly genomic data. The document focuses on describing some freely available databases, analysis tools, and online resources for tasks like sequence analysis, without attempting to provide specific protocols as user needs vary. These resources range from programs on graduate student web pages to large, complex databases maintained by government agencies.
This document summarizes some of the computational tools and resources available for plant genome informatics. It introduces how bioinformatics has grown to help biologists analyze and extract meaning from large amounts of biological data, particularly genomic data. The document focuses on describing some freely available databases, analysis tools, and online resources for tasks like sequence analysis, without attempting to provide specific protocols as user needs vary. These resources range from programs on graduate student web pages to large, complex databases maintained by government agencies.
This document summarizes some of the computational tools and resources available for plant genome informatics. It introduces how bioinformatics has grown to help biologists analyze and extract meaning from large amounts of biological data, particularly genomic data. The document focuses on describing some freely available databases, analysis tools, and online resources for tasks like sequence analysis, without attempting to provide specific protocols as user needs vary. These resources range from programs on graduate student web pages to large, complex databases maintained by government agencies.
This document summarizes some of the computational tools and resources available for plant genome informatics. It introduces how bioinformatics has grown to help biologists analyze and extract meaning from large amounts of biological data, particularly genomic data. The document focuses on describing some freely available databases, analysis tools, and online resources for tasks like sequence analysis, without attempting to provide specific protocols as user needs vary. These resources range from programs on graduate student web pages to large, complex databases maintained by government agencies.
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