Next-generation sequencing and sequence data analysis / authored by, Kuo Ping Chiu, associate research fellow/associate professor, Genomics Research Center, Academia Sinica, National Taiwan University, National Central University, Taiwan.

Format:

Book

Author/Creator:

Chiu, Kuo Ping, author.

Language:

English

Subjects (All):

Machine learning.

Computational intelligence.

Data mining.

Physical Description:

1 online resource (160 p.)

Edition:

1st ed.

Place of Publication:

Sharjah : Bentham Science Publishers, Limited, [2015]

Summary:

Nucleic acid sequencing techniques have enabled researchers to determine the exact order of base pairs - and by extension the information present - in the genome of living organisms. Consequently our understanding of this information and its link to genetic expression at molecular and cellular levels has lead to rapid advances in biology genetics biotechnology and medicine. Next-Generation Sequencing and Sequence Data Analysis is a brief primer on DNA sequencing techniques and methods used to analyze sequence data. Readers will learn about recent concepts and methods in genomics such as sequence library preparation cluster generation for PCR technologies PED sequencing genome assembly exome sequencing transcriptomics and more. This book serves as a textbook for students undertaking courses in bioinformatics and laboratory methods in applied biology. General readers interested in learning about DNA sequencing techniques may also benefit from the simple format of information presented in the book.

Contents:

CONTENTS; FOREWORD ; PREFACE ; ACKNOWLEDGEMENTS ; CONFLICT OF INTEREST; Background Introduction ; The Ultimate Frontier of Knowledge: the Myster-ious Genomes and the Gene Expression and Regul-ation in the Upstream of Biological Information Flow ; INTRODUCTION; MICROSCOPIC STRUCTURE AND ORGANIZATION OF INFORMATION MOLECULES; THE STRUCTURE AND ORGANIZATION OF INFORMATION MOLECULES AT THE MOLECULAR LEVEL; DNA is the Most Magnificent Molecule Selected By Evolution ; DNA Packaging; Nucleosome; GENE EXPRESSION AND REGULATION IN THE EUKARYOTIC SYSTEM

A. ATP-Dependent and ATP-Independent Chromatin Remodeling EnzymeB. X Chromosome Inactivation; C. Pathway Flow from Extracellular Signal to the Nucleus; D. TFs, Motifs, and DNA-Protein Interaction; E. Transcription Factories (TFs); F. Epigenetic Modifications; G. Alternative Splicing; H. MicroRNA (miRNA); THE BOTTOM LINE; REFERENCES; Evolution of DNA Sequencing Technologies ; INTRODUCTION; CHARACTERISTICS OF DNA SEQUENCING; ADVANCES IN SEQUENCING TECHNOLOGIES; MANUAL SANGER SEQUENCING; AUTOMATED SANGER SEQUENCING ; KEY CHANGES FROM MANUAL TO AUTOMATED SANGER SEQUE-NCING

THE NEXT-GENERATION SEQUENCING SINGLE MOLECULE SEQUENCING; REFERENCES; Mechanisms of Next-Generation Sequencing (NGS) ; INTRODUCTION; Changes Made From Automated Sanger Sequencing to Next-Gen Sequencing; In situ PCR for Clonal Amplification of Templates; NGS Sequencing Mechanisms; I. Sequencing-By-Synthesis; Solexa Sequencers Manufactured By Illumina - HiSeq 2000 as an Example (Fig. 1); Sequencing Library Preparation ; 454 Sequencers By Roche ; Sequencing Library Preparation; Sequencing-By-Synthesis on Picotiter Plate

II. Sequencing By Ligation: SOLiD Sequencers (Fig. 8) Manufactured By Life Technologies Inc.REFERENCES; Genome Assembly, the Genomic Era and the Rise of the Omics Era ; INTRODUCTION; PART I. REVIEW OF THE STRATEGIES EMPLOYED FOR GENOME ASSEMBLY; Technological impacts on genome assembly; Next-Generation Sequencing (NGS); Oligo-mediated technologies ; PART II. THE GENOMIC ERA; The Human Genome Project; Genomic Era; Post Genomic Era; KEY EVENTS LEADING TO THE DEVELOPMENT OF THE GENOMIC ERA ; GENERAL PROCEDURE FOR RESEQUENCING; ADVANTAGES OF DIRECT MAPPING AGAINST A REFERENCE (NORMAL) GENOME

PART III. THE RISE OF THE OMICS ERAThe Omics Era; REFERENCES; Application of DNA Sequencing in Biological Investigations ; Laboratory Setup and Fundamental Works ; INTRODUCTION; I. WETLAB; Setting up a Wetlab; Protocols to Use; II. DRYLAB ; Setting Up a Drylab; Sequence Data Processing; Methods Used for Sequence Data Processing and Analysis; REFERENCES; Sequencing Libraries and Basic Procedure for Sequencing Library Construction ; INTRODUCTION; CLASSIFICATION OF SEQUENCING LIBRARIES; GENERAL PROCEDURE FOR SEQUENCING LIBRARY CONSTRUCTION

Step I. Libraries Constructed Prior to Sequencing Libraries

Notes:

Includes index.

Description based on online resource; title from PDF title page (ebrary, viewed June 16, 2016).

ISBN:

9781681080925

1681080923

OCLC:

951065345