Saccharinae Bioinformatics Resources
The primary goal of this chapter is to provide practical information for utilizing the array of Saccharinae bioinformatics resources that are presently available. The chapter begins with the description of a survey of Saccharinae bioinformatics resources
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Saccharinae Bioinformatics Resources Alan R. Gingle and F. Alex Feltus
Abstract The primary goal of this chapter is to provide practical information for utilizing the array of Saccharinae bioinformatics resources that are presently available. The chapter begins with the description of a survey of Saccharinae bioinformatics resources that was undertaken early in 2010. Resources are categorized by life science area(s), available data types, and modes of data access. Navigating resources and searching for Saccharinae data is then described through a broad collection of search examples that cover categories ranging from maps, markers, and genomic sequence through transcriptome-, proteome-, and biochemistry-related data. Data integration, as means for providing answers to more complex biological questions, is discussed in terms of existing applications of reference genome sequence and possible future applications of co-expression network data. Keywords Bioinformatics • Co-expression network • Database • Genome • Proteome • Saccharinae • Sorghinae • Transcriptome
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Overview
While some have considered the Saccharinae to be composed of members from 13 genera, including Saccharum, Miscanthus, and Imperata (Clayton and Renvoize 1986), there is growing evidence that supports the merging of the Saccharinae and
A.R. Gingle (*) Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Rd, CAGT, Rm 113, Athens, GA 30602-6810, USA e-mail: [email protected] F.A. Feltus Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA e-mail: [email protected] A.H. Paterson (ed.), Genomics of the Saccharinae, Plant Genetics and Genomics: Crops and Models 11, DOI 10.1007/978-1-4419-5947-8_13, © Springer Science+Business Media New York 2013
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Sorghinae into a single clade (E. Kellogg, Chap. 1 of this volume). With this and inclusiveness in mind, the bioinformatic resource survey and descriptive text of this chapter include resources providing data for either Saccharinae or Sorghinae. Also, for the sake of conciseness, the Saccharinae and Sorghinae clades as well as bioinformatics resources, that provide related data, are referred to as “Saccharinae” in this chapter. The spectrum of Saccharinae bioinformatics resources covers a broad range of life science areas and available data types of both genomic and phenotypic nature. For example, genetic map and diversity data are provided by genetics- and evolutionary biology-related resources, Sorghum genomic sequence views are available at the Joint Genome Initiative (JGI) Web resource and phenotypic data are provided by resources with focus areas, ranging from crop science to biochemistry. In addition, multi-organism resources, such as those at the National Center for Biotechnology Information (NCBI), provide a substantial amount of Saccharinae data that can be searched directly and are also available via links from other resources. Searching bioinformatics resources often involves multiple data types from multiple resources
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