Bioinformatics in Aquaculture Principles and Methods 1st Edition by Zhanjiang John Liu ISBN 1118782356 9781118782354

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Product details:

ISBN 10: 1118782356 

ISBN 13: 9781118782354

Author: Zhanjiang (John) Liu

Bioinformatics derives knowledge from computer analysis of biological data. In particular, genomic and transcriptomic datasets are processed, analysed and, whenever possible, associated with experimental results from various sources, to draw structural, organizational, and functional information relevant to biology. Research in bioinformatics includes method development for storage, retrieval, and analysis of the data.

Bioinformatics in Aquaculture provides the most up to date reviews of next generation sequencing technologies, their applications in aquaculture, and principles and methodologies for the analysis of genomic and transcriptomic large datasets using bioinformatic methods, algorithm, and databases. The book is unique in providing guidance for the best software packages suitable for various analysis, providing detailed examples of using bioinformatic software and command lines in the context of real world experiments.

This book is a vital tool for all those working in genomics, molecular biology, biochemistry and genetics related to aquaculture, and computational and biological sciences.

 

Table of contents: 

 

Part I: Bioinformatics Analysis of Genomic Sequences
Chapter 1 – Introduction to Linux and Command Line Tools for Bioinformatics
Chapter 2 – Determining Sequence Identities: BLAST, Phylogenetic Analysis, and Syntenic Analyses
Chapter 3 – Next-Generation Sequencing Technologies and the Assembly of Short Reads into Reference Genome Sequences
Chapter 4 – Genome Annotation: Determination of the Coding Potential of the Genome
Chapter 5 – Analysis of Repetitive Elements in the Genome
Chapter 6 – Analysis of Duplicated Genes and Multi-Gene Families
Chapter 7 – Dealing with Complex Polyploidy Genomes: Considerations for Assembly and Annotation of the Common Carp Genome

Part II: Bioinformatics Analysis of Transcriptomic Sequences
Chapter 8 – Assembly of RNA-Seq Short Reads into Transcriptome Sequences
Chapter 9 – Analysis of Differentially Expressed Genes and Co-expressed Genes Using RNA-Seq Datasets
Chapter 10 – Gene Ontology, Enrichment Analysis, and Pathway Analysis
Chapter 11 – Genetic Analysis Using RNA-Seq: Bulk Segregant RNA-Seq
Chapter 12 – Analysis of Long Non-coding RNAs
Chapter 13 – Analysis of MicroRNAs and Their Target Genes
Chapter 14 – Analysis of Allele-Specific Expression
Chapter 15 – Bioinformatics Analysis of Epigenetics

Part III: Bioinformatics Mining and Genetic Analysis of DNA Markers
Chapter 16 – Bioinformatics Mining of Microsatellite Markers from Genomic and Transcriptomic Sequences
Chapter 17 – SNP Identification from Next-Generation Sequencing Datasets
Chapter 18 – SNP Array Development, Genotyping, Data Analysis, and Applications
Chapter 19 – Genotyping by Sequencing and Data Analysis: RAD and 2b-RAD Sequencing
Chapter 20 – Bioinformatics Considerations and Approaches for High-Density Linkage Mapping in Aquaculture
Chapter 21 – Genomic Selection in Aquaculture Breeding Programs
Chapter 22 – Quantitative Trait Locus Mapping in Aquaculture Species: Principles and Practice
Chapter 23 – Genome-wide Association Studies of Performance Traits
Chapter 24 – Gene Set Analysis of SNP Data from Genome-wide Association Studies

Part IV: Comparative Genome Analysis
Chapter 25 – Comparative Genomics Using CoGe, Hook, Line, and Sinker: Using CoGe Tools for Catching Fish Genome Evolution

Part V: Bioinformatics Resources, Databases, and Genome Browsers
Chapter 26 – NCBI Resources Useful for Informatics Issues in Aquaculture
Chapter 27 – Resources and Bioinformatics Tools in Ensembl
Chapter 28 – iAnimal: Cyberinfrastructure to Support Data-driven Science

Index

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