Methods in microbiology. Volume 41, New approachs to prokaryotic systematics. / edited by Michael Goodfellow, Iain Sutcliffe, Jongsik Chun.

Format:

Book

Contributor:

Goodfellow, M., editor.

Sutcliffe, Iain, editor.

Chun, Jongsik, editor.

Language:

English

Subjects (All):

Prokaryotes.

Microbiology.

Physical Description:

1 online resource (368 p.)

Place of Publication:

London, [England] ; San Diego, California : Academic Press, 2014.

Language Note:

English

Summary:

Volume 41 of Methods in Microbiology is a methods book designed to highlight procedures that will revitalize the purposes and practices of prokaryotic systematics. This volume will notably show that genomics and computational biology are pivotal to the new direction of travel and will emphasise that new developments need to be built upon historical good practices, notably the continued use of the nomenclatural type concept and the requirement to deposit type strains in at least two service culture collections in different countries. Detailed protocols on cutting edge methodsPrepared by leadin

Contents:

Front Cover; New Approaches to Prokaryotic Systematics; Copyright; Dedication; Contents; Contributors; Preface; Chapter 1: The Need for Change: Embracing the Genome; 1. A brief history of genomic sequencing of prokaryotes; 2. Why Sequence the Genomes of Prokaryotes?; 3. The State-of-the-Art; 4. Where We Are Going; Acknowledgement; References; Chapter 2: An Introduction to Phylogenetics and the Tree of Life; 1. Introduction; 2. Step 1: Posing a question; 3. Step 2: Choosing Relevant Sequences; 3.1. Obtaining 16S rRNA Sequences for Bacteria, Archaea and Eukarya

3.2. A note on the availability and use of data and methods4. Step 3: Aligning Sequences and Editing the Alignment; 5. Step 4: The theory of Fitting and Selecting a Phylogenetic Model; 5.1. Markov nucleotide substitution models; 5.2. Inferring phylogenies under Markov substitution models; 5.3. Frequentist inference; 5.4. Bayesian inference; 5.5. Model comparison and assessment; 5.6. Frequentist methods; 5.7. Bayesian model choice; 6. Step 5: Inferring Trees-Practical Guidelines for fitting and comparing Markov substitution models; 6.1. Alignment formats for phylogeny programs

6.2. Inferring maximum likelihood phylogenies using RAxML6.3. Bayesian analyses with PhyloBayes; 6.4. Posterior predictive checks; 7. Step 6: Interpreting the Phylogenetic Tree; Conclusions; Acknowledgements; References; Chapter 3: The All-Species Living Tree Project; 1. Introduction; 2. Sources of Information; 2.1. Classification of microbial databases; 2.1.1. Taxonomy (LPSN and Bergey's Manual); 2.1.2. Type-strain information (StrainInfo database); 2.1.3. Sequences and alignments (ARB and SILVA); 3. Database creation and updating; 4. Features of the Database

4.1. Optimized SSU and LSU alignments4.2. Curated hierarchical classification; 4.3. Risk-group classification; 4.4. Taxonomic thresholds; 5. Phylogenetic trees; 6. LTP as a Taxonomic Tool; Acknowledgements; References; Chapter 4: 16S rRNA Gene-Based Identification of Bacteria and Archaea using the EzTaxon Server; 1. Introduction; 2. Use of 16S rRNA gene sequences in prokaryotic systematics; 2.1. Sequencing of 16S rRNA genes; 2.2. Calculation of nucleotide sequence similarity values of 16S rRNA gene sequences; 3. Identification of Bacteria Using the EzTaxon Database; 3.1. EzTaxon database

3.2. Algorithm for ``EzTaxon search ́ ́3.3. Overall workflow from Sanger DNA sequence data; 3.4. Assembly and trimming of sequences; 3.5. Manual editing of sequences using the secondary structure information; 3.5.1. Manual editing of sequences with EzEditor; 3.6. Identification of strains using the EzTaxon server; 3.7. Phylogenetic analysis; Concluding remarks; Acknowledgement; References; Chapter 5: Revolutionizing Prokaryotic Systematics Through Next-Generation Sequencing; 1. Introduction; 2. Sequencing Approaches; 3. Bioinformatic Analyses; 3.1. De novo assembly and mapping; 3.2. Annotation

3.3. Comparative genomic analysis

Notes:

Description based upon print version of record.

Includes bibliographical references and index.

Description based on online resource; title from PDF title page (ebrary, viewed December 09, 2014).

ISBN:

0-12-800443-6