Bacterial pangenomics
Subtitle: methods and protocols
By: edited by Alessio Mengoni, Department of Biology, University of Florence, Florence Italy, Marco Galardini, EMBL-EBI, Cambridge, UK, Marco Fondi, Department of Biology, University of Florence, Florence Italy
Contributors: Springer Science+Business Media
Series: Methods in Molecular Biology -- 1231; Springer protocols; Methods in molecular biology (Clifton, N.J.) -- v. 1231.; Springer protocols (Series)
Publisher: Humana Press
Published: 2015
Place of publication: New York, NY
Language: eng
Number of pages: 298
ISBN-13: 9781493917198; 9781493917204
Copyright date: 2015
Subjects: Genetics; Bacteriology; Laboratory Manuals; Bacterial Genome; Bacterial genetics; Bacterial genomes
Notes: Includes bibliographical references and index.
Table of contents: title: Pulsed field gel electrophoresis and genome size estimates -- Rosa Alduina and Annalisa Pisciotta; title: Comparative analyses of extrachromosomal bacterial replicons, identification of chromids, and experimental evaluation of their indispensability  -- Lukasz Dziewit and Dariusz Bartosik; title: Choice of next-generation sequencing pipelines  -- F. Del Chierico [and others]; title: Pyrosequencing protocol for bacterial genomes  -- Ermanno Rizzi; title: Bacterial metabarcoding by 16S rRNA gene ion torrent amplicon sequencing  -- Elio Fantini [and others]; title: Illumina-solexa sequencing protocol for bacterial genomes  -- Zhenfei Hu, Lei Cheng, and Hai Wang; title: High-throughput phenomics  -- Carlo Viti [and others]; title: Comparative analysis of gene expression : uncovering expression conservation and divergence between Salmonella enterica serovar typhimurium strains LT2 and 14028S  -- Paolo Sonego [and others]; title: Raw sequence data and quality control  -- Giovanni Bacci; title: Methods for assembling reads and producing contigs  -- Valerio Orlandini, Marco Fondi, and Renato Fani; title: Mapping contigs using CONTIGuator  -- Marco Galardini, Alessio Mengoni, and Marco Bazzicalupo; title: Gene calling and bacterial genome annotation with BG7  -- Raquel Tobes [and others]; title: Defining orthologs and pangenome size metrics  -- Emanuele Bosi, Renato Fani, and Marco Fondi; title: Robust identification of orthologues and paralogues for microbial pan-genomics using GET_HOMOLOGUES : a case study of pIncA/C plasmids  -- Pablo Vinuesa and Bruno Contreras-Moreira; title: Genome-scale metabolic network reconstruction  -- Marco Fondi and Pietro Liò; title: From pangenome to panphenome and back  -- Marco Galardini, Alessio Mengoni, and Stefano Mocali; title: Genome-wide detection of selection and other evolutionary forces  -- Zhuofei Xu and Rui Zhou; title: Integrated microbial genome resource of analysis -- Alice Checcucci and Alessio Mengoni.