ProbCons: Probabilistic consistency-based multiple sequence alignment

作者: Chuong B Do , Mahathi SP Mahabhashyam , Michael Brudno , Serafim Batzoglou

DOI: 10.1101/GR.2821705

关键词: BiologyArtificial intelligenceComputational problemMultiple sequence alignmentSequence alignmentConsistency (database systems)Benchmark (computing)Machine learningProbabilistic logicSoftwareRange (mathematics)Bioinformatics

摘要: … multiple sequence alignment based on probabilistic consistency, and evaluate its performance on several standard alignment … the Viterbi algorithm only on pairwise alignments, as the …

参考文章(61)
Kazutaka Katoh, Kazuharu Misawa, Kei‐ichi Kuma, Takashi Miyata, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform Nucleic Acids Research. ,vol. 30, pp. 3059- 3066 ,(2002) , 10.1093/NAR/GKF436
C. Notredame, L. Holm, D. G. Higgins, COFFEE: an objective function for multiple sequence alignments Bioinformatics. ,vol. 14, pp. 407- 422 ,(1998) , 10.1093/BIOINFORMATICS/14.5.407
R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Research. ,vol. 32, pp. 1792- 1797 ,(2004) , 10.1093/NAR/GKH340
J. D. Thompson, F. Plewniak, O. Poch, A comprehensive comparison of multiple sequence alignment programs Nucleic Acids Research. ,vol. 27, pp. 2682- 2690 ,(1999) , 10.1093/NAR/27.13.2682
Marco Punta, Penny C Coggill, Ruth Y Eberhardt, Jaina Mistry, John Tate, Chris Boursnell, Ningze Pang, Kristoffer Forslund, Goran Ceric, Jody Clements, Andreas Heger, Liisa Holm, Erik LL Sonnhammer, Sean R Eddy, Alex Bateman, Robert D Finn, None, The Pfam protein families database Nucleic Acids Research. ,vol. 30, pp. 276- 280 ,(2000) , 10.1093/NAR/GKR1065
S. Henikoff, J. G. Henikoff, Amino acid substitution matrices from protein blocks Proceedings of the National Academy of Sciences of the United States of America. ,vol. 89, pp. 10915- 10919 ,(1992) , 10.1073/PNAS.89.22.10915
Steven E Brenner, Patrice Koehl, Michael Levitt, The ASTRAL compendium for protein structure and sequence analysis Nucleic Acids Research. ,vol. 28, pp. 254- 256 ,(2000) , 10.1093/NAR/28.1.254
J. Michael Sauder, Jonathan W. Arthur, Roland L. Dunbrack Jr., Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins. ,vol. 40, pp. 6- 22 ,(2000) , 10.1002/(SICI)1097-0134(20000701)40:1<6::AID-PROT30>3.0.CO;2-7
I. N. Shindyalov, P. E. Bourne, Protein Structure Alignment by Incremental Combinatorial Extension (CE) of the Optimal Path Protein Engineering. ,vol. 11, pp. 739- 747 ,(1998) , 10.1093/PROTEIN/11.9.739
David T Jones, PROTEIN SECONDARY STRUCTURE PREDICTION BASED ON POSITION-SPECIFIC SCORING MATRICES Journal of Molecular Biology. ,vol. 292, pp. 195- 202 ,(1999) , 10.1006/JMBI.1999.3091