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فهرست مطالب: Preface . . . . . . . . . . . . . . vContributors. . . . . . . . . . . . . . . ix PART I PHYLOGENETICS AND EVOLUTION 1 Orthology Prediction and Phylogenetic Analysis Methods in Plants. . . . . . . . . . 3 Abdoallah Sharaf and Sawsan Elateek 2 Species Tree Inference with SNP Data . . . . . . . 23 Michael Matschiner 3 High-Throughput Evolutionary Comparative Analysis of Long Intergenic Noncoding RNAs in Multiple Organisms . . . . 45 Anna C. Nelson Dittrich and Andrew D. L. Nelson 4 NGS-Indel Coder v2.0: A Streamlined Pipeline to Code Indel Characters in Phylogenomic Data . . . . . . . . . . . 61 Julien Boutte, Mark Fishbein, and Shannon C. K. Straub 5 An SGSGeneloss-Based Method for Constructing a Gene Presence–Absence Table Using Mosdepth . . . . . . . . 73 Cassandria G. Tay Fernandez, Jacob I. Marsh, Benjamin J. Nestor, Mitchell Gill, Agnieszka A. Golicz, Philipp E. Bayer, and David Edwards 6 POInT: A Tool for Modeling Ancient Polyploidies Using Multiple Polyploid Genomes . . . . . . . . . . . . . 81 Yue Hao and Gavin C. Conant PART II OMICS ANALYSIS 7 Searching for Homologous Genes Using Daisychain . . . . 95 Philipp E. Bayer and David Edwards 8 Detecting MicroRNAs in Plant Genomes with miRkwood . . . . 103 Sylvain Legrand, Isabelle Guigon, and He´le`ne Touzet 9 Pangenome Analysis of Plant Transcripts and Coding Sequences. . . . 121 Bruno Contreras-Moreira, A´ lvaro Rodrı´guez del Rı´o, Carlos P. Cantalapiedra, Rube´n Sancho, and Pablo Vinuesa 10 Metagenomics Bioinformatic Pipeline . . . . . . . 153 Diego Garfias-Gallegos, Claudia Zirion-Martı´nez, Edder D. Bustos-Dı´az, Tania Vanessa Arellano-Ferna´ndez, Jose´ Abel Lovaco-Flores, Aaron Espinosa-Jaime, J. Abraham Avelar-Rivas, and Nelly Se´lem-Mojica 11 Rhizosphere and Endosphere Bacterial Communities Survey by Metagenomics Approach. . . . . . . . . . . 181 Victoria Mesa vii12 Applying Synteny Networks (SynNet) to Study Genomic Arrangements of Protein-Coding Genes in Plants. . . . . . . 199 Samuel David Gamboa-Tuz, Alejandro Pereira-Santana, Tao Zhao, and M. Eric Schranz 13 Plant In Situ Hi-C Experimental Protocol and Bioinformatic Analysis . . . . . . . . . . . . 217 Francisco J. Pe´rez-de los Santos, Jesu´ s Emiliano Sotelo-Fonseca, Ame´rica Ramı´rez-Colmenero, Hans-Wilhelm Nu¨tzmann, Selene L. Fernandez-Valverde, and Katarzyna Oktaba 14 Isolation of Boechera stricta Developing Embryos for Hi-C . . . 249 Mariana Tiscaren˜o-Andrade, Katarzyna Oktaba, and Jean-Philippe Vielle-Calzada PART III EXPERIMENTAL PROCEDURES FOR TRAIT CHARACTERIZATION 15 Discovering the Secrets of Ancient Plants: Recovery of DNA from Museum and Archaeological Plant Specimens . . . . . 261 Oscar Estrada, Stephen M. Richards, and James Breen 16 Use of Allele-Specific Amplification for Rapid Identification of Aromatic and Non-aromatic Rice Germplasms . . . . . . . 269 Debarati Chakraborty 17 Efficient Protein Extraction Protocols for NanoLC-MS/MS Proteomics Analysis of Plant Tissues with High Proteolytic Activity: A Case Study with Pineapple Pulp . . . . . . . . . . . . . 281 Esau´ Bojorquez-Vela´zquez, Jose´ M. Elizalde-Contreras, Jesu´ s Alejandro Zamora-Brisen˜o, and Eliel Ruiz-May Index . . . . . . . . . . . . . . . 291 مشخصات فایل |
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| عنوان (Title): | Plant Comparative Genomics |
| نام فایل (File name): | 924-www.GeneProtocols.ir-Plant Comparative Genomics-Humana (2022).pdf |
| عنوان فارسی (Title in Persian): | ژنومیک مقایسه ای گیاهی |
| ایجاد کننده: | Alejandro Pereira-Santana, Samuel David Gamboa-Tuz, Luis Carlos Rodríguez-Zapata |
| زبان (Language): | انگلیسی English |
| سال انتشار: | 2022 |
| شابک ISBN: | 1071624288, 9781071624289 |
| نوع سند (Doc. type): | کتاب |
| فرمت (File extention): | |
| حجم فایل (File size): | 8.97 مگابایت |
| تعداد صفحات (Book length in pages): | 293 |
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برچسب ها:
2022,
انگلیسی,
بیوانفورماتیک,
پروتکل آزمایشگاهی,
پروتکل ژنتیک,
پروتکل گیاهی,
ژنوم,
ژنومیکس,
گیاه شناسی,
