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PROMALS3D: Multiple Protein Sequence Alignment Enhanced with Evolutionary and Three-Dimensional Structural Information 由 Jimin Pei, Nick V. Grishin

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Fast and sensitive multiple alignment of large genomic sequences 由 Michael Brudno, Michael A. Chapman, Berthold Göttgens, Serafim Batzoglou, Burkhard Morgenstern

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Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints 由 Robin D. Dowell, Sean R. Eddy

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Approximate protein structural alignment in polynomial time 由 Rachel Kolodny, Nathan Linial

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OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy 由 Gajendra P. S. Raghava, Stephen M. J. Searle, Patrick C. Audley, Jonathan D. Barber, Geoffrey J. Barton

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Kalign – an accurate and fast multiple sequence alignment algorithm 由 Timo Lassmann, Erik L. L. Sonnhammer

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Prediction of Protein Structure by Evaluation of Sequence-structure Fitness 由 Christos Ouzounis, Chris Sander, Michael E. Scharf, Reinhard Schneider

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Improving the accuracy of protein secondary structure prediction using structural alignment 由 Scott Montgomerie, Shan Sundararaj, Warren J. Gallin, David S. Wishart

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DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment 由 A R Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann, Burkhard Morgenstern

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Multiple sequence alignment for phylogenetic purposes 由 David A. Morrison

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transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences 由 Olaf R. P. Bininda‐Emonds

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Accelerated probabilistic inference of RNA structure evolution 由 Ian Holmes

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DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment 由 Erik S. Wright

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MRFalign: Protein Homology Detection through Alignment of Markov Random Fields 由 Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu

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MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons 由 Sven Siebert, Rolf Backofen

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Assessment of the ability to model proteins with leucine‐rich repeats in light of the latest structural information 由 Andrey V. Kajava, Boštjan Kobe

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Profile analysis: detection of distantly related proteins. 由 Michael Gribskov, A. McLachlan, David Eisenberg

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HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database 由 Lucy Stebbings

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A new size‐independent score for pairwise protein structure alignment and its application to structure classification and nucleic‐acid binding prediction 由 Yuedong Yang, Jian Zhan, Huiying Zhao, Yaoqi Zhou

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MUSTER: Improving protein sequence profile–profile alignments by using multiple sources of structure information 由 Sitao Wu, Yang Zhang

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