Exploring familial relationships using multiple sequence alignment.
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[1] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[2] N. Guex,et al. SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling , 1997, Electrophoresis.
[3] M. Sternberg,et al. Prediction of protein secondary structure and active sites using the alignment of homologous sequences. , 1987, Journal of molecular biology.
[4] M. Kimura,et al. The neutral theory of molecular evolution. , 1983, Scientific American.
[5] N. Saitou,et al. The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.
[6] P. K. Mehta,et al. A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70% , 1995, Protein science : a publication of the Protein Society.
[7] W. Fitch,et al. Construction of phylogenetic trees. , 1967, Science.
[8] Sean R. Eddy,et al. Multiple Alignment Using Hidden Markov Models , 1995, ISMB.
[9] M. O. Dayhoff,et al. Establishing homologies in protein sequences. , 1983, Methods in enzymology.
[10] Jaap Heringa,et al. OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity , 1992, Comput. Appl. Biosci..
[11] M. Sternberg,et al. A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons. , 1987, Journal of molecular biology.
[12] A A Salamov,et al. Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignments. , 1995, Journal of molecular biology.
[13] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[14] Rolf Apweiler,et al. The SWISS-PROT protein sequence data bank and its supplement TrEMBL , 1997, Nucleic Acids Res..
[15] C. Heizmann,et al. Intracellular calcium-binding proteins: more sites than insights. , 1991, Trends in biochemical sciences.
[16] H. Kawasaki,et al. Classification and evolution of EF-hand proteins , 1998, Biometals.
[17] P. Argos,et al. Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence. , 1996, Protein engineering.
[18] B. Rost,et al. Prediction of protein secondary structure at better than 70% accuracy. , 1993, Journal of molecular biology.
[19] I. D. Campbell,et al. Key residues involved in calcium-binding motifs in EGF-like domains , 1991, Nature.
[20] Olivier Poch,et al. BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs , 1999, Bioinform..
[21] Robert D. Finn,et al. Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins , 1999, Nucleic Acids Res..
[22] Evelyn Camon,et al. The EMBL Nucleotide Sequence Database , 2000, Nucleic Acids Res..
[23] D. Higgins,et al. SAGA: sequence alignment by genetic algorithm. , 1996, Nucleic acids research.
[24] H. Kawasaki,et al. Calcium-binding proteins. 1: EF-hands. , 1994, Protein profile.
[25] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[26] M S Waterman,et al. Identification of common molecular subsequences. , 1981, Journal of molecular biology.
[27] Olivier Poch,et al. A comprehensive comparison of multiple sequence alignment programs , 1999, Nucleic Acids Res..
[28] O. Gotoh. Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. , 1996, Journal of molecular biology.
[29] Hans-Werner Mewes,et al. The PIR-International Protein Sequence Database , 1992, Nucleic Acids Res..
[30] P. D. Smith,et al. Structural evolution of the annexin supergene family. , 1994, Trends in genetics : TIG.
[31] J. Felsenstein. CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.
[32] M. P. Fernández,et al. Annexin gene structures and molecular evolutionary genetics , 1997, Cellular and Molecular Life Sciences CMLS.
[33] M. O. Dayhoff,et al. Atlas of protein sequence and structure , 1965 .
[34] P. Argos,et al. SRS: information retrieval system for molecular biology data banks. , 1996, Methods in enzymology.
[35] Jun S. Liu,et al. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. , 1993, Science.
[36] J. Felsenstein. Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. , 1996, Methods in enzymology.
[37] M. A. McClure,et al. Hidden Markov models of biological primary sequence information. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[38] D. Lipman,et al. The multiple sequence alignment problem in biology , 1988 .
[39] Jaap Heringa,et al. Two Strategies for Sequence Comparison: Profile-preprocessed and Secondary Structure-induced Multiple Alignment , 1999, Comput. Chem..
[40] P. Argos,et al. A method to recognize distant repeats in protein sequences , 1993, Proteins.
[41] J. Adachi,et al. MOLPHY version 2.3 : programs for molecular phylogenetics based on maximum likelihood , 1996 .
[42] R. King,et al. Identification and application of the concepts important for accurate and reliable protein secondary structure prediction , 1996, Protein science : a publication of the Protein Society.
[43] Susumu Nakayama,et al. Evolution of EF-hand calcium-modulated proteins. II. Domains of several subfamilies have diverse evolutionary histories , 1992, Journal of Molecular Evolution.
[44] S. Altschul,et al. A tool for multiple sequence alignment. , 1989, Proceedings of the National Academy of Sciences of the United States of America.
[45] S. Henikoff,et al. Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[46] Liisa Holm,et al. COFFEE: an objective function for multiple sequence alignments , 1998, Bioinform..
[47] G. Gonnet,et al. Exhaustive matching of the entire protein sequence database. , 1992, Science.
[48] Amos Bairoch,et al. The PROSITE database, its status in 2002 , 2002, Nucleic Acids Res..
[49] M. P. Fernández,et al. Distinct Annexin Subfamilies in Plants and Protists Diverged Prior to Animal Annexins and from a Common Ancestor , 1997, Journal of Molecular Evolution.
[50] T. Blundell,et al. Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.
[51] J. Thompson,et al. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.
[52] A. Dress,et al. Multiple DNA and protein sequence alignment based on segment-to-segment comparison. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[53] D. Haussler,et al. Hidden Markov models in computational biology. Applications to protein modeling. , 1993, Journal of molecular biology.
[54] P. Argos,et al. Seventy‐five percent accuracy in protein secondary structure prediction , 1997, Proteins.