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(Download PDF) Bioinformatics in Aquaculture Principles and Methods 1St Edition Zhanjiang John Liu Online Ebook All Chapter PDF
(Download PDF) Bioinformatics in Aquaculture Principles and Methods 1St Edition Zhanjiang John Liu Online Ebook All Chapter PDF
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Bioinformatics in Aquaculture
Bioinformatics in Aquaculture
All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or
transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise,
except as permitted by law. Advice on how to obtain permission to reuse material from this title is available
at http://www.wiley.com/go/permissions.
The right of Zhanjiang (John) Liu to be identified as the author of the editorial material in this work has been
asserted in accordance with law.
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10 9 8 7 6 5 4 3 2 1
v
Contents
PhyloCSF 188
CPAT 189
Homology Search 190
Homology Protein Search 191
Homology Domain Search 191
ORF Length Trimming (Optional) 193
UTR Region Trimming 194
Analysis of lncRNA Expression 194
Analysis and Prediction of lncRNA Functions 194
Future Perspectives 196
References 196
Peak-calling 257
DMR Identification 257
Gene Expression Analysis 260
DMR Annotation and Functional Prediction 261
Other Ways of Analysis for Methylation 263
Histone Modifications and Bioinformatics 264
Histone Modifications 264
Data Analysis 265
Perspectives 265
References 266
the intention of the editor or the book chapter contributors to provide bioinformatics
guidance on topics such as programming. Rather, the focus is on providing a basic
framework about the need for informatics analysis, and then to provide guidance on
the practical applications of existing bioinformatics tools for aquaculture problems.
This book has 28 chapters, arranged in five parts. Part 1 focuses on issues of dealing
with DNA sequences: basic command lines (Chapter 1); how to determine sequence
identities (Chapter 2); how to assemble short read sequences into contigs and scaffolds
(Chapter 3); how to annotate genome sequences (Chapter 4); how to analyze repetitive
sequences (Chapter 5); how to analyze duplicated genes (Chapter 6); and how to deal
with complex genomes such as tetraploid fish genomes (Chapter 7). Part 2 focuses on the
issues involved in dealing with RNA sequences: how to assemble short reads of RNA-Seq
into transcriptome sequences (Chapter 8); how to identify differentially expressed genes
and co-regulated genes (Chapter 9); how to characterize results from RNA-Seq analysis
using gene ontology, enrichment analysis, and gene pathways (Chapter 10); how to
use RNA-Seq for genetic analysis (Chapter 11); analysis of long non-coding RNAs
(Chapter 12); analysis of microRNAs and their target genes (Chapter 13); determination
of allele-specific gene expression (Chapter 14); and epigenetic analysis (Chapter 15).
Part 3 focuses on the issues involved in the discovery and application of molecular
markers: microsatellites (Chapter 16); single-nucleotide polymorphisms (SNPs)
(Chapter 17); SNP arrays (Chapter 18); genotyping by sequencing (Chapter 19); genetic
linkage analysis (Chapter 20); genome selection (Chapter 21); QTL mapping (Chapter
22); GWAS (Chapter 23); and gene pathway analysis in GWAS (Chapter 24). Part 4
focuses on the issues involved in comparative genome analysis: comparative genomics
using CoGe (Chapter 25). The last part, Part 5, introduces bioinformatics resources,
databases, and genome browsers useful for aquaculture, such as NCBI resources
and tools (Chapter 26); Ensembl resources and tools (Chapter 27); and the iAnimal
bioinformatics infrastructures (Chapter 28).
This book was written to illustrate both principles and detailed methods. It should be
useful to academic professionals, research scientists, graduate students and college stu-
dents in agriculture, as well as students of aquaculture and fisheries. In particular, this
book should be a good textbook for graduate training classes. I am grateful to all the
contributors for their inputs; it is their great experience and efforts that made this book
possible. In addition, I am grateful to the postdoctoral fellows and graduate students in
my laboratory at Auburn University for recognizing the need for and inspiring the pro-
duction of such a “manual-like” book, but with sufficient background for beginner-level
graduate students. Also, I have had a pleasant experience interacting with Kevin Met-
thews (senior project editor) and Ramya Raghavan (project editor) of Wiley-Blackwell
Publishing.
During the course of writing and editing this book, I have worked extremely hard
to fulfill my responsibilities as the associate provost and associate vice president for
research, while performing my duty and passion as a professor and graduate advisor.
As a consequence, I have fallen short of fulfilling my responsibility as a father to my
three lovely daughters—Elise, Lisa, and Lena Liu—and even more so to my granddaugh-
ter Evelyn Wong. I wish to express my appreciation for their independence and great
progress.
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Title: Gold
A play in four acts
Language: English
Credits: Mary Glenn Krause, Chuck Greif and the Online Distributed
Proofreading Team at https://www.pgdp.net (This file was
produced from images generously made available by The
Internet Archive)
PLAYS BY
EUGENE G. O’NEILL
————
THE MOON OF THE
CARIBBEES
and Six Other Plays of
the Sea
BEYOND THE
HORIZON
THE STRAW
GOLD
Gold
A PLAY IN FOUR ACTS
BY
EUGENE G. O’NEILL
Copyright, 1920, by
Boni & Liveright, Inc.