ProbCons: Probabilistic consistency-based multiple sequence alignment.
暂无分享,去创建一个
[1] P. Sneath,et al. Numerical Taxonomy , 1962, Nature.
[2] Andrew J. Viterbi,et al. Error bounds for convolutional codes and an asymptotically optimum decoding algorithm , 1967, IEEE Trans. Inf. Theory.
[3] S. B. Needleman,et al. A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.
[4] C. Metz. Basic principles of ROC analysis. , 1978, Seminars in nuclear medicine.
[5] M. O. Dayhoff,et al. 22 A Model of Evolutionary Change in Proteins , 1978 .
[6] M S Waterman,et al. Identification of common molecular subsequences. , 1981, Journal of molecular biology.
[7] O. Gotoh. An improved algorithm for matching biological sequences. , 1982, Journal of molecular biology.
[8] N. Saitou,et al. The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.
[9] Eugene W. Myers,et al. Optimal alignments in linear space , 1988, Comput. Appl. Biosci..
[10] D. Lipman,et al. The multiple sequence alignment problem in biology , 1988 .
[11] S F Altschul,et al. Weights for data related by a tree. , 1989, Journal of molecular biology.
[12] Martin Vingron,et al. A fast and sensitive multiple sequence alignment algorithm , 1989, Comput. Appl. Biosci..
[13] P. Argos,et al. Determination of reliable regions in protein sequence alignments. , 1990, Protein engineering.
[14] O. Gotoh. Consistency of optimal sequence alignments. , 1990, Bulletin of Mathematical Biology.
[15] P. Argos,et al. Motif recognition and alignment for many sequences by comparison of dot-matrices. , 1991, Journal of molecular biology.
[16] W. Miller,et al. A time-efficient, linear-space local similarity algorithm , 1991 .
[17] S. Altschul. Amino acid substitution matrices from an information theoretic perspective , 1991, Journal of Molecular Biology.
[18] Peter J. Munson,et al. A novel randomized iterative strategy for aligning multiple protein sequences , 1991, Comput. Appl. Biosci..
[19] 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.
[20] G. Gonnet,et al. Exhaustive matching of the entire protein sequence database. , 1992, Science.
[21] Kun-Mao Chao,et al. Locating well-conserved regions within a pairwise alignment , 1993, Comput. Appl. Biosci..
[22] John D. Kececioglu,et al. The Maximum Weight Trace Problem in Multiple Sequence Alignment , 1993, CPM.
[23] C. Sander,et al. The FSSP database of structurally aligned protein fold families. , 1994, Nucleic acids research.
[24] M S Waterman,et al. Sequence alignment and penalty choice. Review of concepts, case studies and implications. , 1994, Journal of molecular biology.
[25] B. Rost,et al. Combining evolutionary information and neural networks to predict protein secondary structure , 1994, Proteins.
[26] Moon-Jung Chung,et al. Multiple sequence alignment using simulated annealing , 1994, Comput. Appl. Biosci..
[27] D. Haussler,et al. Hidden Markov models in computational biology. Applications to protein modeling. , 1993, Journal of molecular biology.
[28] 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.
[29] Sean R. Eddy,et al. Multiple Alignment Using Hidden Markov Models , 1995, ISMB.
[30] S. Miyazawa. A reliable sequence alignment method based on probabilities of residue correspondences. , 1995, Protein engineering.
[31] A G Murzin,et al. SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.
[32] S. Wodak,et al. Optimal protein structure alignments by multiple linkage clustering: application to distantly related proteins. , 1995, Protein engineering.
[33] D. Higgins,et al. SAGA: sequence alignment by genetic algorithm. , 1996, Nucleic acids research.
[34] 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.
[36] 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.
[37] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[38] Ian Holmes,et al. Dynamic programming alignment accuracy , 1998, RECOMB '98.
[39] Burkhard Morgenstern,et al. DIALIGN: finding local similarities by multiple sequence alignment , 1998, Bioinform..
[40] P E Bourne,et al. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. , 1998, Protein engineering.
[41] Durbin,et al. Biological Sequence Analysis , 1998 .
[42] Liisa Holm,et al. COFFEE: an objective function for multiple sequence alignments , 1998, Bioinform..
[43] Sean R. Eddy,et al. Pfam: multiple sequence alignments and HMM-profiles of protein domains , 1998, Nucleic Acids Res..
[44] John P. Overington,et al. HOMSTRAD: A database of protein structure alignments for homologous families , 1998, Protein science : a publication of the Protein Society.
[45] Olivier Poch,et al. A comprehensive comparison of multiple sequence alignment programs , 1999, Nucleic Acids Res..
[46] B. Rost. Twilight zone of protein sequence alignments. , 1999, Protein engineering.
[47] D T Jones,et al. Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.
[48] Olivier Poch,et al. BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs , 1999, Bioinform..
[49] G. Church,et al. Alignment and structure prediction of divergent protein families: periplasmic and outer membrane proteins of bacterial efflux pumps. , 1999, Journal of molecular biology.
[50] J. M. Sauder,et al. Large‐scale comparison of protein sequence alignment algorithms with structure alignments , 2000, Proteins.
[51] Patrice Koehl,et al. The ASTRAL compendium for protein structure and sequence analysis , 2000, Nucleic Acids Res..
[52] M. Lässig,et al. Finite-temperature sequence alignment. , 1999, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.
[53] Terri K. Attwood,et al. The PRINTS Database: A Resource for Identification of Protein Families , 2002, Briefings Bioinform..
[54] K. Katoh,et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.
[55] Maximilian Schlosshauer,et al. A novel approach to local reliability of sequence alignments , 2002, Bioinform..
[56] Adam Godzik,et al. In search for more accurate alignments in the twilight zone , 2002, Protein science : a publication of the Protein Society.
[57] Tatiana A. Tatusova,et al. NCBI Reference Sequence Project: update and current status , 2003, Nucleic Acids Res..
[58] Michael Lappe,et al. Accurate detection of very sparse sequence motifs , 2003, RECOMB '03.
[59] Lode Wyns,et al. Align-m-a new algorithm for multiple alignment of highly divergent sequences , 2004, Bioinform..
[60] Michael Brudno,et al. PROBCONS: Probabilistic Consistency-Based Multiple Alignment of Amino Acid Sequences , 2004, AAAI.
[61] Fyodor A Kondrashov,et al. The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint. , 2004, Genome research.
[62] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[63] M. Waterman,et al. Comparative biosequence metrics , 2005, Journal of Molecular Evolution.
[64] R. Doolittle,et al. Progressive sequence alignment as a prerequisitetto correct phylogenetic trees , 2007, Journal of Molecular Evolution.