Cargando…

New Approaches to Prokaryotic Systematics /

Volume 41 of <i>Methods in Microbiology</i> 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...

Descripción completa

Detalles Bibliográficos
Clasificación:Libro Electrónico
Otros Autores: Goodfellow, M. (Editor ), Sutcliffe, Iain (Editor ), Chun, Jongsik (Editor )
Formato: Electrónico eBook
Idioma:Inglés
Publicado: London : Elsevier/Academic Press, 2014.
Edición:First edition.
Colección:Methods in microbiology ; v. 41.
Temas:
Acceso en línea:Texto completo

MARC

LEADER 00000cam a2200000Ii 4500
001 SCIDIR_ocn897115960
003 OCoLC
005 20231120111917.0
006 m o d
007 cr cnu|||unuuu
008 141201s2014 enka ob 001 0 eng d
040 |a N$T  |b eng  |e rda  |e pn  |c N$T  |d EBLCP  |d YDXCP  |d OCLCO  |d N$T  |d UIU  |d OPELS  |d IDEBK  |d DEBSZ  |d NRC  |d OCLCO  |d OCLCQ  |d DEBBG  |d OCLCA  |d MEU  |d CUS  |d OCLCF  |d D6H  |d AU@  |d OCLCQ  |d OCLCO  |d OCLCQ  |d CASUM  |d OCLCO 
019 |a 899560965 
020 |a 9780128004432  |q (electronic bk.) 
020 |a 0128004436  |q (electronic bk.) 
020 |z 9780128001769 
020 |z 0128001763 
035 |a (OCoLC)897115960  |z (OCoLC)899560965 
050 4 |a QH445.2  |b N48 2014eb 
060 4 |a QW 51 
072 7 |a SCI  |x 008000  |2 bisacsh 
072 7 |a SCI  |x 045000  |2 bisacsh 
082 0 4 |a 579.3/135  |2 23 
245 0 0 |a New Approaches to Prokaryotic Systematics /  |c edited by Michael Goodfellow, Iain Sutcliffe, Jongsik Chun. 
250 |a First edition. 
264 1 |a London :  |b Elsevier/Academic Press,  |c 2014. 
300 |a 1 online resource (xix, 327 pages) :  |b illustrations. 
336 |a text  |b txt  |2 rdacontent 
337 |a computer  |b c  |2 rdamedia 
338 |a online resource  |b cr  |2 rdacarrier 
490 1 |a Methods in microbiology ;  |v volume 41 
546 |a Text in English. 
504 |a Includes bibliographical references and index. 
588 0 |a Online resource; title from HTML table of contents page (ScienceDirect, viewed May 25, 2018). 
505 0 |a 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. 
505 8 |a 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. 
505 8 |a 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. 
505 8 |a 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. 
505 8 |a 3.2. Algorithm for &#xFFFD;&#xFFFD;EzTaxon search&#xFFFD;&#xFFFD;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. 
520 |a Volume 41 of <i>Methods in Microbiology</i> 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. <br><br><ul><li>Detailed protocols on cutting edge me. 
650 0 |a Prokaryotes  |x Genome mapping. 
650 0 |a Prokaryotes  |x Genetics. 
650 2 |a Bacteria  |x genetics  |0 (DNLM)D001419Q000235 
650 6 |a Procaryotes  |0 (CaQQLa)201-0065825  |x Cartes chromosomiques.  |0 (CaQQLa)201-0379954 
650 6 |a Procaryotes  |0 (CaQQLa)201-0065825  |x G&#xFFFD;en&#xFFFD;etique.  |0 (CaQQLa)201-0380134 
650 7 |a SCIENCE  |x Life Sciences  |x Biology.  |2 bisacsh 
650 7 |a SCIENCE  |x Life Sciences  |x Microbiology.  |2 bisacsh 
650 7 |a Prokaryotes  |x Genetics  |2 fast  |0 (OCoLC)fst01078854 
655 4 |a Internet Resources. 
700 1 |a Goodfellow, M.,  |e editor. 
700 1 |a Sutcliffe, Iain,  |e editor. 
700 1 |a Chun, Jongsik,  |e editor. 
776 0 8 |i Print version:  |t New approaches to prokaryotic systematics.  |b First edition.  |d London : Elsevier/Academic Press, 2014  |z 0128001763  |z 9780128001769  |w (OCoLC)889647159 
830 0 |a Methods in microbiology ;  |v v. 41. 
856 4 0 |u https://sciencedirect.uam.elogim.com/science/book/9780128001769  |z Texto completo