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. Dynamic programming -- O. Ufuk Nalbantoglu Heuristic alignment methods -- Osamu Gotoh Objective functions -- Haluk Dogan and Hasan H. Otu Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment -- Stefano Iantorno ... [et al.] BLAST and FASTA similarity searching for multiple sequence alignment -- William R. Pearson 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 Magi ... [et al.] 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 Loytynoja 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 SATe -- 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. "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. Front Matter....Pages i-xii Front Matter....Pages 1-1 Front Matter....Pages 3-27 Back Matter....Pages 29-43 ....Pages 45-58
