Statistical compression of protein sequences and inference of marginal probability landscapes over competing alignments using finite state models and Dirichlet priors
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Lloyd Allison | Arun S Konagurthu | Dinithi Sumanaweera | A. Konagurthu | L. Allison | Dinithi Sumanaweera | D. Sumanaweera | A. S. Konagurthu
[1] G J Barton,et al. Evaluation and improvements in the automatic alignment of protein sequences. , 1987, Protein engineering.
[2] N. Sloane,et al. On the Voronoi Regions of Certain Lattices , 1984 .
[3] Erik L. L. Sonnhammer,et al. Kalign – an accurate and fast multiple sequence alignment algorithm , 2005, BMC Bioinformatics.
[4] F E Cohen,et al. Pairwise sequence alignment below the twilight zone. , 2001, Journal of molecular biology.
[5] Thomas D. Cuypers,et al. Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase , 2012, Genome Biology.
[6] Rodrigo Lopez,et al. Clustal W and Clustal X version 2.0 , 2007, Bioinform..
[7] Michael S. Rosenberg,et al. Sequence alignment : methods, models, concepts, and strategies , 2009 .
[8] R. Doolittle. Of urfs and orfs : a primer on how to analyze devised amino acid sequences , 1986 .
[9] A G Murzin,et al. SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.
[10] Sang Joon Kim,et al. A Mathematical Theory of Communication , 2006 .
[11] C. S. Wallace,et al. Coding Decision Trees , 1993, Machine Learning.
[12] Trevor I. Dix,et al. Compression and Approximate Matching , 1999, Comput. J..
[13] T. Smith,et al. Optimal sequence alignments. , 1983, Proceedings of the National Academy of Sciences of the United States of America.
[14] Trevor I. Dix,et al. Modelling-Alignment for Non-random Sequences , 2004, Australian Conference on Artificial Intelligence.
[15] M. O. Dayhoff,et al. Atlas of protein sequence and structure , 1965 .
[16] P. Argos,et al. An assessment of amino acid exchange matrices in aligning protein sequences: the twilight zone revisited. , 1995, Journal of molecular biology.
[17] Serafim Batzoglou,et al. CONTRAlign: Discriminative Training for Protein Sequence Alignment , 2006, RECOMB.
[18] Steven A Benner,et al. Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments. , 2004, Journal of molecular biology.
[19] Arthur M. Lesk,et al. Introduction to Protein Science: Architecture, Function, and Genomics , 2001 .
[20] C. S. Wallace,et al. Statistical and Inductive Inference by Minimum Message Length (Information Science and Statistics) , 2005 .
[21] 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.
[22] Sean R. Eddy,et al. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids , 1998 .
[23] Cathy H. Wu,et al. UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..
[24] C. S. Wallace,et al. Estimation and Inference by Compact Coding , 1987 .
[25] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[26] M S Waterman,et al. Sequence alignment and penalty choice. Review of concepts, case studies and implications. , 1994, Journal of molecular biology.
[27] Tal Pupko,et al. A Simulation‐Based Approach to Statistical Alignment , 2018, Systematic biology.
[28] G. Gonnet,et al. Empirical and structural models for insertions and deletions in the divergent evolution of proteins. , 1993, Journal of molecular biology.
[29] P. Argos,et al. Analysis of insertions/deletions in protein structures. , 1992, Journal of molecular biology.
[30] A. Löytynoja,et al. Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis , 2008, Science.
[31] K. Katoh,et al. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.
[32] Andrei N. Kolmogorov,et al. On Tables of Random Numbers (Reprinted from "Sankhya: The Indian Journal of Statistics", Series A, Vol. 25 Part 4, 1963) , 1998, Theor. Comput. Sci..
[33] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[34] Peter Grünwald,et al. Invited review of the book Statistical and Inductive Inference by Minimum Message Length , 2006 .
[35] Lloyd Allison,et al. Coding Ockham's Razor , 2018, Springer International Publishing.
[36] W. C. Barker. Of URFs and ORFs: A primer on how to analyze derived amino acid sequences: Russell F. Doolittle, University Science Books, Mill Valley, CA. Paperback. Under $15 , 1987 .
[37] Jun Zhu,et al. Bayesian adaptive sequence alignment algorithms , 1998, Bioinform..
[38] D. Higgins,et al. T-Coffee: A novel method for fast and accurate multiple sequence alignment. , 2000, Journal of molecular biology.
[39] Lode Wyns,et al. SABmark- a benchmark for sequence alignment that covers the entire known fold space , 2005, Bioinform..
[40] C. S. Wallace,et al. An Information Measure for Classification , 1968, Comput. J..
[41] Chuong B. Do,et al. ProbCons: Probabilistic consistency-based multiple sequence alignment. , 2005, Genome research.
[42] Elena Rivas,et al. Parameterizing sequence alignment with an explicit evolutionary model , 2015, BMC Bioinformatics.
[43] M. O. Dayhoff,et al. 22 A Model of Evolutionary Change in Proteins , 1978 .
[44] Peter J. Stuckey,et al. Statistical inference of protein structural alignments using information and compression , 2016, bioRxiv.
[45] M. Suchard,et al. Joint Bayesian estimation of alignment and phylogeny. , 2005, Systematic biology.
[46] Lloyd Allison,et al. The Bits Between Proteins , 2018, 2018 Data Compression Conference.
[47] G. Gonnet,et al. Exhaustive matching of the entire protein sequence database. , 1992, Science.
[48] C. S. Wallace,et al. Finite-state models in the alignment of macromolecules , 1992, Journal of Molecular Evolution.
[49] Cristina Cattaneo,et al. Introduction to genomics. , 2012, Methods in molecular biology.