Zhanjiang (John) Liu is currently the Associate Provost and Associate Vice President for Research at Auburn University, and a Professor in the School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, USA.

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• About the Editor xxiiiList of Contributors xxvPreface xxxiPart I Bioinformatics Analysis of Genomic Sequences 11 Introduction to Linux and Command Line Tools for Bioinformatics 3Shikai Liu and Zhanjiang Liu2 Determining Sequence Identities: BLAST, Phylogenetic Analysis, and Syntenic Analyses 30Sen Gao, Zihao Yuan, Ning Li, Jiaren Zhang and Zhanjiang Liu3 Next-Generation Sequencing Technologies and the Assembly of Short Reads into Reference Genome Sequences 43Ning Li, Xiaozhu Wang and Zhanjiang Liu4 Genome Annotation: Determination of the Coding Potential of the Genome 74Ruijia Wang, Lisui Bao, Shikai Liu and Zhanjiang Liu5 Analysis of Repetitive Elements in the Genome 86Lisui Bao and Zhanjiang Liu6 Analysis of Duplicated Genes andMulti-Gene Families 98Ruijia Wang and Zhanjiang Liu7 Dealing with Complex Polyploidy Genomes: Considerations for Assembly and Annotation of the Common Carp Genome 110Peng Xu, Jiongtang Li and Xiaowen SunPart II Bioinformatics Analysis of Transcriptomic Sequences 1238 Assembly of RNA-Seq Short Reads into Transcriptome Sequences 125Jun Yao, Chen Jiang, Chao Li, Qifan Zeng and Zhanjiang Liu9 Analysis of Differentially Expressed Genes and Co-expressed Genes Using RNA-Seq Datasets 135Chao Li, Qifan Zeng, Chen Jiang, Jun Yao and Zhanjiang Liu10 Gene Ontology, Enrichment Analysis, and Pathway Analysis 150Tao Zhou, Jun Yao and Zhanjiang Liu11 Genetic Analysis Using RNA-Seq: Bulk Segregant RNA-Seq 169Jun Yao, RuijiaWang and Zhanjiang Liu12 Analysis of Long Non-coding RNAs 179Ruijia Wang, Lisui Bao, Shikai Liu and Zhanjiang Liu13 Analysis of MicroRNAs and Their Target Genes 200Shikai Liu and Zhanjiang Liu14 Analysis of Allele-Specific Expression 228Yun Li, Ailu Chen and Zhanjiang Liu15 Bioinformatics Analysis of Epigenetics 247Yanghua He and Jiuzhou SongPart III Bioinformatics Mining and Genetic Analysis of DNA Markers 27516 Bioinformatics Mining of Microsatellite Markers from Genomic and Transcriptomic Sequences 277Shaolin Wang, Yanliang Jiang and Zhanjiang Liu17 SNP Identification from Next-Generation Sequencing Datasets 288Qifan Zeng, Luyang Sun, Qiang Fu, Shikai Liu and Zhanjiang Liu18 SNP Array Development, Genotyping, Data Analysis, and Applications 308Shikai Liu, Qifan Zeng, Xiaozhu Wang and Zhanjiang Liu19 Genotyping by Sequencing and Data Analysis: RAD and 2b-RAD Sequencing 338Shi Wang, Jia Lv, Jinzhuang Dou, Qianyun Lu, Lingling Zhang and Zhenmin Bao20 Bioinformatics Considerations and Approaches for High-Density Linkage Mapping in Aquaculture 356Yun Li, Shikai Liu, Ruijia Wang, Zhenkui Qin and Zhanjiang Liu21 Genomic Selection in Aquaculture Breeding Programs 380Mehar S. Khatkar22 Quantitative Trait Locus Mapping in Aquaculture Species: Principles and Practice 392Alejandro P. Gutierrez and Ross D. Houston23 Genome-wide Association Studies of Performance Traits 415Xin Geng, Degui Zhi and Zhanjiang Liu24 Gene Set Analysis of SNP Data from Genome-wide Association Studies 434Shikai Liu, Peng Zeng and Zhanjiang LiuPart IV Comparative Genome Analysis 46125 Comparative Genomics Using CoGe, Hook, Line, and Sinker 463Blake Joyce, Asher Baltzell, Matt Bomhoff and Eric Lyons26 NCBI Resources Useful for Informatics Issues in Aquaculture 491Zihao Yuan, Yujia Yang, Shikai Liu and Zhanjiang Liu27 Resources and Bioinformatics Tools in Ensembl 508Yulin Jin, Suxu Tan, Jun Yao and Zhanjiang Liu28 iAnimal: Cyberinfrastructure to Support Data-driven Science 527Blake Joyce, Asher Baltzell, Fiona McCarthy, Matt Bomhoff and Eric LyonsConclusion 544Acknowledgments 545References 545Index 547

Zhanjiang (John) Liu is currently the Associate Provost and Associate Vice President for Research at Auburn University, and a Professor in the School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, USA.

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• About the Editor xxiiiList of Contributors xxvPreface xxxiPart I Bioinformatics Analysis of Genomic Sequences 11 Introduction to Linux and Command Line Tools for Bioinformatics 3Shikai Liu and Zhanjiang Liu2 Determining Sequence Identities: BLAST, Phylogenetic Analysis, and Syntenic Analyses 30Sen Gao, Zihao Yuan, Ning Li, Jiaren Zhang and Zhanjiang Liu3 Next-Generation Sequencing Technologies and the Assembly of Short Reads into Reference Genome Sequences 43Ning Li, Xiaozhu Wang and Zhanjiang Liu4 Genome Annotation: Determination of the Coding Potential of the Genome 74Ruijia Wang, Lisui Bao, Shikai Liu and Zhanjiang Liu5 Analysis of Repetitive Elements in the Genome 86Lisui Bao and Zhanjiang Liu6 Analysis of Duplicated Genes andMulti-Gene Families 98Ruijia Wang and Zhanjiang Liu7 Dealing with Complex Polyploidy Genomes: Considerations for Assembly and Annotation of the Common Carp Genome 110Peng Xu, Jiongtang Li and Xiaowen SunPart II Bioinformatics Analysis of Transcriptomic Sequences 1238 Assembly of RNA-Seq Short Reads into Transcriptome Sequences 125Jun Yao, Chen Jiang, Chao Li, Qifan Zeng and Zhanjiang Liu9 Analysis of Differentially Expressed Genes and Co-expressed Genes Using RNA-Seq Datasets 135Chao Li, Qifan Zeng, Chen Jiang, Jun Yao and Zhanjiang Liu10 Gene Ontology, Enrichment Analysis, and Pathway Analysis 150Tao Zhou, Jun Yao and Zhanjiang Liu11 Genetic Analysis Using RNA-Seq: Bulk Segregant RNA-Seq 169Jun Yao, RuijiaWang and Zhanjiang Liu12 Analysis of Long Non-coding RNAs 179Ruijia Wang, Lisui Bao, Shikai Liu and Zhanjiang Liu13 Analysis of MicroRNAs and Their Target Genes 200Shikai Liu and Zhanjiang Liu14 Analysis of Allele-Specific Expression 228Yun Li, Ailu Chen and Zhanjiang Liu15 Bioinformatics Analysis of Epigenetics 247Yanghua He and Jiuzhou SongPart III Bioinformatics Mining and Genetic Analysis of DNA Markers 27516 Bioinformatics Mining of Microsatellite Markers from Genomic and Transcriptomic Sequences 277Shaolin Wang, Yanliang Jiang and Zhanjiang Liu17 SNP Identification from Next-Generation Sequencing Datasets 288Qifan Zeng, Luyang Sun, Qiang Fu, Shikai Liu and Zhanjiang Liu18 SNP Array Development, Genotyping, Data Analysis, and Applications 308Shikai Liu, Qifan Zeng, Xiaozhu Wang and Zhanjiang Liu19 Genotyping by Sequencing and Data Analysis: RAD and 2b-RAD Sequencing 338Shi Wang, Jia Lv, Jinzhuang Dou, Qianyun Lu, Lingling Zhang and Zhenmin Bao20 Bioinformatics Considerations and Approaches for High-Density Linkage Mapping in Aquaculture 356Yun Li, Shikai Liu, Ruijia Wang, Zhenkui Qin and Zhanjiang Liu21 Genomic Selection in Aquaculture Breeding Programs 380Mehar S. Khatkar22 Quantitative Trait Locus Mapping in Aquaculture Species: Principles and Practice 392Alejandro P. Gutierrez and Ross D. Houston23 Genome-wide Association Studies of Performance Traits 415Xin Geng, Degui Zhi and Zhanjiang Liu24 Gene Set Analysis of SNP Data from Genome-wide Association Studies 434Shikai Liu, Peng Zeng and Zhanjiang LiuPart IV Comparative Genome Analysis 46125 Comparative Genomics Using CoGe, Hook, Line, and Sinker 463Blake Joyce, Asher Baltzell, Matt Bomhoff and Eric Lyons26 NCBI Resources Useful for Informatics Issues in Aquaculture 491Zihao Yuan, Yujia Yang, Shikai Liu and Zhanjiang Liu27 Resources and Bioinformatics Tools in Ensembl 508Yulin Jin, Suxu Tan, Jun Yao and Zhanjiang Liu28 iAnimal: Cyberinfrastructure to Support Data-driven Science 527Blake Joyce, Asher Baltzell, Fiona McCarthy, Matt Bomhoff and Eric LyonsConclusion 544Acknowledgments 545References 545Index 547

Zhanjiang (John) Liu is currently the Associate Provost and Associate Vice President for Research at Auburn University, and a Professor in the School of Fisheries, Aquaculture and Aquatic Sciences, and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, USA.

Select Guide Rating

• About the Editor xxiiiList of Contributors xxvPreface xxxiPart I Bioinformatics Analysis of Genomic Sequences 11 Introduction to Linux and Command Line Tools for Bioinformatics 3Shikai Liu and Zhanjiang Liu2 Determining Sequence Identities: BLAST, Phylogenetic Analysis, and Syntenic Analyses 30Sen Gao, Zihao Yuan, Ning Li, Jiaren Zhang and Zhanjiang Liu3 Next-Generation Sequencing Technologies and the Assembly of Short Reads into Reference Genome Sequences 43Ning Li, Xiaozhu Wang and Zhanjiang Liu4 Genome Annotation: Determination of the Coding Potential of the Genome 74Ruijia Wang, Lisui Bao, Shikai Liu and Zhanjiang Liu5 Analysis of Repetitive Elements in the Genome 86Lisui Bao and Zhanjiang Liu6 Analysis of Duplicated Genes andMulti-Gene Families 98Ruijia Wang and Zhanjiang Liu7 Dealing with Complex Polyploidy Genomes: Considerations for Assembly and Annotation of the Common Carp Genome 110Peng Xu, Jiongtang Li and Xiaowen SunPart II Bioinformatics Analysis of Transcriptomic Sequences 1238 Assembly of RNA-Seq Short Reads into Transcriptome Sequences 125Jun Yao, Chen Jiang, Chao Li, Qifan Zeng and Zhanjiang Liu9 Analysis of Differentially Expressed Genes and Co-expressed Genes Using RNA-Seq Datasets 135Chao Li, Qifan Zeng, Chen Jiang, Jun Yao and Zhanjiang Liu10 Gene Ontology, Enrichment Analysis, and Pathway Analysis 150Tao Zhou, Jun Yao and Zhanjiang Liu11 Genetic Analysis Using RNA-Seq: Bulk Segregant RNA-Seq 169Jun Yao, RuijiaWang and Zhanjiang Liu12 Analysis of Long Non-coding RNAs 179Ruijia Wang, Lisui Bao, Shikai Liu and Zhanjiang Liu13 Analysis of MicroRNAs and Their Target Genes 200Shikai Liu and Zhanjiang Liu14 Analysis of Allele-Specific Expression 228Yun Li, Ailu Chen and Zhanjiang Liu15 Bioinformatics Analysis of Epigenetics 247Yanghua He and Jiuzhou SongPart III Bioinformatics Mining and Genetic Analysis of DNA Markers 27516 Bioinformatics Mining of Microsatellite Markers from Genomic and Transcriptomic Sequences 277Shaolin Wang, Yanliang Jiang and Zhanjiang Liu17 SNP Identification from Next-Generation Sequencing Datasets 288Qifan Zeng, Luyang Sun, Qiang Fu, Shikai Liu and Zhanjiang Liu18 SNP Array Development, Genotyping, Data Analysis, and Applications 308Shikai Liu, Qifan Zeng, Xiaozhu Wang and Zhanjiang Liu19 Genotyping by Sequencing and Data Analysis: RAD and 2b-RAD Sequencing 338Shi Wang, Jia Lv, Jinzhuang Dou, Qianyun Lu, Lingling Zhang and Zhenmin Bao20 Bioinformatics Considerations and Approaches for High-Density Linkage Mapping in Aquaculture 356Yun Li, Shikai Liu, Ruijia Wang, Zhenkui Qin and Zhanjiang Liu21 Genomic Selection in Aquaculture Breeding Programs 380Mehar S. Khatkar22 Quantitative Trait Locus Mapping in Aquaculture Species: Principles and Practice 392Alejandro P. Gutierrez and Ross D. Houston23 Genome-wide Association Studies of Performance Traits 415Xin Geng, Degui Zhi and Zhanjiang Liu24 Gene Set Analysis of SNP Data from Genome-wide Association Studies 434Shikai Liu, Peng Zeng and Zhanjiang LiuPart IV Comparative Genome Analysis 46125 Comparative Genomics Using CoGe, Hook, Line, and Sinker 463Blake Joyce, Asher Baltzell, Matt Bomhoff and Eric Lyons26 NCBI Resources Useful for Informatics Issues in Aquaculture 491Zihao Yuan, Yujia Yang, Shikai Liu and Zhanjiang Liu27 Resources and Bioinformatics Tools in Ensembl 508Yulin Jin, Suxu Tan, Jun Yao and Zhanjiang Liu28 iAnimal: Cyberinfrastructure to Support Data-driven Science 527Blake Joyce, Asher Baltzell, Fiona McCarthy, Matt Bomhoff and Eric LyonsConclusion 544Acknowledgments 545References 545Index 547