Title Multiple sequence alignment methods / edited by David J. Russell, Department of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA

Published New York ; Heidelberg ; Dordrecht ; London : Humana Press, [2014] ©2014

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Description 1 online resource (xii, 287 pages) : illustrations (some color) Series Methods in Molecular Biology, 1940-6029 ; Volume No. 1079 Methods in molecular biology (Clifton, N.J.) ; v. 1079. 1064-3745 Contents Part I. Theory -- Dynamic programming / Ö. Ufuk Nalbantoğlu -- Heuristic alignment methods / Osamu Gotoh -- Objective functions / Haluk Doğan and Hasan H. Otu -- Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment / Stefano Iantorno, Kevin Gori, Nick Goldman, Manuel Gil, and Christophe Dessimoz -- BLAST and FASTA similarity searching for multiple sequence alignment / William R. Pearson Part I. Alignment Techniques -- Clustal omega, accurate alignment of very large numbers of sequences / Fabian Sievers and Desmond G. Higgins -- T-coffee : tree-based consistency objective function for alignment evaluation / Cedrik Magis, Jean-François Taly, Giovanni Bussotti, Jia-Ming Chang, Paolo Di Tommaso, Ionas Erb, José Espinosa-Carrasco, and Cedric Notredame -- MAFFT : iterative refinement and additional methods / Kazutaka Katoh and Daron M. Standley -- Multiple sequence alignment using probcons and probalign / Usman Roshan -- Phylogeny-aware alignment with PRANK / Ari Löytynoja -- GramAlign : fast alignment driven by grammar-based phylogeny / David J. Russell -- Multiple sequence alignment with DIALIGN / Burkhard Morgenstern -- PicXAA : a probabilistic scheme for finding the maximum expected accuracy alignment of multiple biological sequences / Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon -- Multiple protein sequence alignment with MSAProbs / Yongchao Liu and Bertil Schmidt -- Large-scale multiple sequence alignment and tree estimation using SATé / Kevin Liu and Tandy Warnow -- PRALINE : a versatile multiple sequence alignment toolkit / Punto Bawono and Jaap Heringa -- PROMALS3D : multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information / Jimin Pei and Nick V. Grishin -- MSACompro : improving multiple protein sequence alignment by predicted structural features / Xin Deng and Jianlin Cheng Summary "From basic performing of sequence alignment through a proficiency at understanding how most industry-standard alignment algorithms achieve their results, Multiple Sequence Alignment Methods describes numerous algorithms and their nuances in chapters written by the experts who developed these algorithms. The various multiple sequence alignment algorithms presented in this handbook give a flavor of the broad range of choices available for multiple sequence alignment generation, and their diversity is a clear reflection of the complexity of the multiple sequence alignment problem and the amount of information that can be obtained from multiple sequence alignments. Each of these chapters not only describes the algorithm it covers but also presents instructions and tips on using their implementation, as is fitting with its inclusion in the highly successful Methods in Molecular Biology series. Authoritative and practical, Multiple Sequence Alignment Methods provides a readily available resource which will allow practitioners to experiment with different algorithms and find the particular algorithm that is of most use in their application."--Publisher's description Bibliography Includes bibliographical references and index Notes English Online resource; title from PDF title page (Springer Protocols, viewed January 30, 2014) Subject Sequence alignment (Bioinformatics) -- Laboratory manuals Computational biology -- Laboratory manuals Genetics -- Technique. Biology. Life sciences. Physical sciences. Information storage and retrieval systems. Sequence alignment (Bioinformatics) Methodology. Publication Formats Genetic Techniques Biology Databases, Genetic Investigative Techniques Databases, Factual Biological Science Disciplines Publication Characteristics Analytical, Diagnostic and Therapeutic Techniques and Equipment Databases as Topic Natural Science Disciplines Information Systems Disciplines and Occupations Information Storage and Retrieval Medical Informatics Applications Information Science Medical Informatics Sequence Alignment Databases, Protein Methods Computational Biology Handbooks biology. biological sciences. physical sciences. methodology. Physical sciences Methodology Life sciences Information storage and retrieval systems Genetics -- Technique Biology Computational biology Sequence alignment (Bioinformatics) Genre/Form Laboratory manuals Laboratory manuals. Manuels de laboratoire. Form Electronic book Author Russell, David James, editor ISBN 9781627036467 1627036466 1627036458 9781627036450

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