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Plant bioinformatics : methods and protocols / edited by David Edwards.

Contributor(s): Material type: TextTextSeries: Methods in molecular biology (Clifton, N.J.) ; v. 1374.Publication details: Totowa, N.J. : Humana Press : Springer, ©2016.Edition: 2nd edDescription: 1 online resource (xi, 365 pages) : illustrations (some color)Content type:
  • text
Media type:
  • computer
Carrier type:
  • online resource
ISBN:
  • 9781493931675
  • 1493931679
Subject(s): Genre/Form: Additional physical formats: Print version:: Plant bioinformatics.DDC classification:
  • 572.8/2 23
LOC classification:
  • QK981
  • QK1-989
NLM classification:
  • W1
  • QK 981
Online resources:
Contents:
Using GenBank / Eric W. Sayers and Ilene Karsch-Mizrachi -- UniProtKB/Swiss-Prot, the manually annotated section of the UniProt knowledgebase : how to use the entry view / Emmanuel Boutet [and others] -- KEGG bioinformatics resource for plant genomics and metabolomics / Minoru Kanehisa -- Plant pathway databases / Pankaj Jaiswal and Björn Usadel -- Plant ontology : a tool for plant genomics / Laurel Cooper and Pankaj Jaiswal -- Ensembl plants : integrating tools for visualizing, mining, and analyzing plant genomics data / Dan Bolser [and others] -- Gramene : a resource for comparative analysis of plants genomes and pathways / Marcela Karey Tello-Ruiz [and others] -- PGSB/MIPS plant genome information resources and concepts for the analysis of complex grass genomes / Manuel Spannagl [and others] -- MaizeGDB : the maize genetics and genomics database / Lisa Harper [and others] -- WheatGenome.info : a resource for wheat genomics resource / Kaitao Lai -- User guidelines for the brassica database : BRAD / Xiaobo Wang, Feng Cheng, and Xiaowu Wang -- TAG sequence identification of genomic regions using TAGdb / Pradeep Ruperao -- Short read alignment using SOAP2 / Bhavna Hurgobin -- Tablet : visualizing next-generation sequence assemblies and mappings / Iain Milne [and others] -- Analysis of genotyping-by-sequencing (GBS) data / Sateesh Kagale [and others] -- Skim-based genotyping by sequencing using a double haploid population to call SNPs, infer gene conversions, and improve genome assemblies / Philipp Emanuel Bayer -- Finding and characterizing repeats in plant genomes / Jacques Nicolas, Pierre Peterlongo, and Sébastien Tempel -- Analysis of RNA-Seq data using TopHat and cufflinks / Sreya Ghosh and Chon-Kit Kenneth Chan.
Summary: The second edition of this volume focuses on applied bioinformatics with specific applications to crops and model plants. Plant Bioinformatics: Methods and Protocols is aimed at plant biologists who have an interest in, or requirement for, accessing and manipulating huge amounts of data being generated by high throughput technologies. This book would also be of interest to bioinformaticians and computer scientists who would benefit from an introduction to the different tools and systems available for plant research. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and software, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and thorough, Plant Bioinformatics: Methods and Protocols helps researchers with the increasing volume and diversity of data from different plants and also the integration of multiple diverse forms of data.
Holdings
Item type Current library Collection Call number Status Date due Barcode Item holds
eBook eBook e-Library eBook Protocols Available
Total holds: 0

Includes bibliographical references and index.

Using GenBank / Eric W. Sayers and Ilene Karsch-Mizrachi -- UniProtKB/Swiss-Prot, the manually annotated section of the UniProt knowledgebase : how to use the entry view / Emmanuel Boutet [and others] -- KEGG bioinformatics resource for plant genomics and metabolomics / Minoru Kanehisa -- Plant pathway databases / Pankaj Jaiswal and Björn Usadel -- Plant ontology : a tool for plant genomics / Laurel Cooper and Pankaj Jaiswal -- Ensembl plants : integrating tools for visualizing, mining, and analyzing plant genomics data / Dan Bolser [and others] -- Gramene : a resource for comparative analysis of plants genomes and pathways / Marcela Karey Tello-Ruiz [and others] -- PGSB/MIPS plant genome information resources and concepts for the analysis of complex grass genomes / Manuel Spannagl [and others] -- MaizeGDB : the maize genetics and genomics database / Lisa Harper [and others] -- WheatGenome.info : a resource for wheat genomics resource / Kaitao Lai -- User guidelines for the brassica database : BRAD / Xiaobo Wang, Feng Cheng, and Xiaowu Wang -- TAG sequence identification of genomic regions using TAGdb / Pradeep Ruperao -- Short read alignment using SOAP2 / Bhavna Hurgobin -- Tablet : visualizing next-generation sequence assemblies and mappings / Iain Milne [and others] -- Analysis of genotyping-by-sequencing (GBS) data / Sateesh Kagale [and others] -- Skim-based genotyping by sequencing using a double haploid population to call SNPs, infer gene conversions, and improve genome assemblies / Philipp Emanuel Bayer -- Finding and characterizing repeats in plant genomes / Jacques Nicolas, Pierre Peterlongo, and Sébastien Tempel -- Analysis of RNA-Seq data using TopHat and cufflinks / Sreya Ghosh and Chon-Kit Kenneth Chan.

The second edition of this volume focuses on applied bioinformatics with specific applications to crops and model plants. Plant Bioinformatics: Methods and Protocols is aimed at plant biologists who have an interest in, or requirement for, accessing and manipulating huge amounts of data being generated by high throughput technologies. This book would also be of interest to bioinformaticians and computer scientists who would benefit from an introduction to the different tools and systems available for plant research. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and software, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and thorough, Plant Bioinformatics: Methods and Protocols helps researchers with the increasing volume and diversity of data from different plants and also the integration of multiple diverse forms of data.

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