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書名 Data production and analysis in population genomics [electronic resource] : methods and protocols / edited by François Pompanon and Aurélie Bonin
出版項 New York : Humana Press, c2012
國際標準書號 9781617798702 (electronic bk.)
1617798703 (electronic bk.)
book jacket
說明 1 online resource (xi, 337 p.) : ill
系列 Methods in molecular biology, 1940-6029 ; 888
Methods in molecular biology ; 888
附註 Includes bibliographical references and index
Pt. I. Sampling and experimental design. Sampling in landscape genomics / Stéphanie Manel, Cécile H. Albert, and Nigel G. Yoccoz -- OligoTag: a program for designing sets of tags for next-generation sequencing of multiplexed samples / Eric Coissac -- SNP Discovery in non-model organisms using 454 next generation sequencing / Christopher W. Wheat -- In Silico Fingerprinting (ISIF): a user-friendly In Silico AFLP program / Margot Paris and Laurence Després -- Pt. II. Producing data. Diversity arrays technology: a generic genome profiling technology on open platforms / Andrzej Kilian, Peter Wenzl, Eric Huttner, Jason Carling, Ling Xia, Hélène Blois, Vanessa Caig, Katarzyna Heller-Uszynska, Damian Jaccoud, Colleen Hopper, Malgorzata Aschenbrenner-Kilian, Margaret Evers, Kaiman Peng, Cyril Cayla, Puthick Hok, and Grzegorz Uszynski -- Two methods to easily obtain nucleotide sequences from AFLP loci of interest / Margot Paris, Claire-Lise Meyer, Christelle Blassiau, Eric Coissac, Pierre Taberlet, and Laurence Després -- Roche Genome Sequencer FLX based high-throughput sequencing of ancient DNA / David E. Alquezar-Planas and Sarah L. Fordyce -- Preparation of normalized cDNA libraries for 454 titanium transcriptome sequencing / Zhao Lai, Yi Zou, Nolan C. Kane, Jeong-Hyeon Choi, Xinguo Wang, and Loren H. Rieseberg -- RAD paired-end sequencing for local de novo assembly and SNP discovery in non-model organisms / Paul D. Etter and Eric Johnson -- Pt. III. Analyzing data. Automated scoring of AFLPs using RawGeno v 2.0, a free R CRAN library / Nils Arrigo, Rolf Holderegger, and Nadir Alvarez -- Haplotype inference / Olivier Delaneau and Jean-François Zagury -- Allele identification in assembled genomic sequence datasets / Katrina M. Dlugosch and Aurélie Bonin -- Multiple testing in large-scale genetic studies / Matthieu Bouaziz, Marine Jeanmougin, and Mickaël Guedj -- Population genomic analysis of model and nonmodel organisms using sequenced RAD tags / Paul A. Hohenlohe, Julian Catchen, and William A. Cresko -- Analysis and management of gene and allelic diversity in subdivided populations using the software program METAPOP / Andrés Pérez-Figueroa, Silvia T. Rodríguez-Ramilo, and Armando Caballero -- DETSEL: An R-Package to detect marker loci responding to selection / Renaud Vitalis -- Use of qualitative environmental and phenotypic variables in the context of allele distribution models: detecting signatures of selection in the genome of lake victoria cichilds / Stéphane Joost, Michael Kalbermatten, Etienne Bezault, and Ole Seehausen -- Genomic scan as a tool for assessing the genetic component of phenotypic variance in wild populations / Carlos M. Herrera
Description based on online resource; title from PDF title page (Springer Protocols, viewed Oct. 12, 2012)
Population genomics is a recently emerged discipline, which aims at understanding how evolutionary processes influence genetic variation across genomes. Today, in the era of cheaper next-generation sequencing, it is no longer as daunting to obtain whole genome data for any species of interest and population genomics is now conceivable in a wide range of fields, from medicine and pharmacology to ecology and evolutionary biology. However, because of the lack of reference genome and of enough a priori data on the polymorphism, population genomics analyses will still involve higher constraints for researchers working on non-model organisms, as regards the choice of the genotyping/sequencing technique or that of the analysis methods. Therefore, Data Production and Analysis in Population Genomics purposely puts emphasis on protocols and methods that are applicable to species where genomic resources are still scarce. It is divided into three convenient sections, each one tackling one of the main challenges facing scientists setting up a population genomics study. The first section helps devising a sampling and/or experimental design suitable to address the biological question of interest. The second section addresses how to implement the best genotyping or sequencing method to obtain the required data given the time and cost constraints as well as the other genetic resources already available. Finally, the last section is about making the most of the (generally huge) dataset produced by using appropriate analysis methods in order to reach a biologically relevant conclusion. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, advice on methodology and implementation, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Data Production and Analysis in Population Genomics serves a wide readership by providing guidelines to help choose and implement the best experimental or analytical strategy for a given purpose
鏈接 Print version: Data production and analysis in population genomics. New York : Humana Press, c2012 9781617798696 (DLC) 2012937649 (OCoLC)775406110
主題 Metagenomics -- Laboratory manuals
Metagenomics -- methods
Metagenomics -- methods -- Laboratory Manuals
Medicine
Human genetics
Nucleic acids
Statistical methods
Biomedicine
Nucleic Acid Chemistry
Biostatistics
Electronic books
Alt Author Pompanon, François, 1966-
Bonin, Aurélie, 1979-
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