genomic sequence alignment Uncertainty in homology inferences : Assessing and improving data

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[1]  A. Krogh.  Two methods for improving performance of an HMM application for gene finding , 1997 .

[2]  C. Lawrence,et al.  RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. , 2005, RNA.

[3]  Ari Löytynoja,et al.  An algorithm for progressive multiple alignment of sequences with insertions. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Jotun Hein,et al.  A nucleotide substitution model with nearest-neighbour interactions , 2004, ISMB/ECCB.

[5]  Lior Pachter,et al.  MAVID: constrained ancestral alignment of multiple sequences. , 2003, Genome research.

[6]  S F Altschul,et al.  Locally optimal subalignments using nonlinear similarity functions. , 1986, Bulletin of mathematical biology.

[7]  Anders Krogh,et al.  Two Methods for Improving Performance of a HMM and their Application for Gene Finding , 1997, ISMB.

[8]  Chuong B. Do,et al.  alignment ProbCons : Probabilistic consistency-based multiple sequence data , 2005 .

[9]  M. I. Kanehisa,et al.  Pattern recognition in nucleic acid sequences. I. A general method for finding local homologies and symmetries , 1982, Nucleic Acids Res..

[10]  Colin N. Dewey,et al.  Evolution at the nucleotide level: the problem of multiple whole-genome alignment. , 2006, Human molecular genetics.

[11]  O. F. Christensen,et al.  Pseudo-likelihood for Non-reversible Nucleotide Substitution Models with Neighbour Dependent Rates , 2006, Statistical applications in genetics and molecular biology.

[12]  I. Holmes,et al.  A "Long Indel" model for evolutionary sequence alignment. , 2003, Molecular biology and evolution.

[13]  D. Haussler,et al.  Aligning multiple genomic sequences with the threaded blockset aligner. , 2004, Genome research.

[14]  Chris P. Ponting,et al.  Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model , 2005, PLoS Comput. Biol..

[15]  Christopher B. Burge,et al.  DNA sequence evolution with neighbor-dependent mutation , 2001, RECOMB '02.

[16]  M. Zuker.  Suboptimal sequence alignment in molecular biology. Alignment with error analysis. , 1991, Journal of molecular biology.

[17]  Kun-Mao Chao,et al.  Locating well-conserved regions within a pairwise alignment , 1993, Comput. Appl. Biosci..

[18]  Chuong B. Do,et al.  Access the most recent version at doi: 10.1101/gr.926603 References , 2003 .

[19]  Gerton Lunter,et al.  Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes , 2007, ISMB/ECCB.

[20]  Ian H. Holmes,et al.  Studies in Probabilistic Sequence Alignment and Evolution , 1998 .

[21]  X. R. L N K C Z V E A Y H G U T X R L N K C Z V E A Y H.  [General method]. , 2000, Diabetes & metabolism.

[22]  Dennis R. Livesay,et al.  Probalign: multiple sequence alignment using partition function posterior probabilities , 2006, Bioinform..

[23]  T. Kunkel,et al.  Deletion errors generated during replication of CAG repeats. , 1999, Nucleic acids research.

[24]  Erik L. L. Sonnhammer,et al.  Automatic assessment of alignment quality , 2005, Nucleic acids research.

[25]  E. Challis.  Measuring the Accuracy of the Neural Code , 2007 .

[26]  T. Jukes.  CHAPTER 24 – Evolution of Protein Molecules , 1969 .

[27]  D. Higgins,et al.  See Blockindiscussions, Blockinstats, Blockinand Blockinauthor Blockinprofiles Blockinfor Blockinthis Blockinpublication Clustal: Blockina Blockinpackage Blockinfor Blockinperforming Multiple Blockinsequence Blockinalignment Blockinon Blockina Minicomputer Article Blockin Blockinin Blockin , 2022 .

[28]  Alfonso Valencia,et al.  Predicting reliable regions in protein alignments from sequence profiles. , 2003, Journal of molecular biology.

[29]  D. Haussler,et al.  Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. , 2003, Molecular biology and evolution.

[30]  Piero Fariselli,et al.  A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins , 2005, BMC Bioinformatics.

[31]  H. Kishino,et al.  Dating of the human-ape splitting by a molecular clock of mitochondrial DNA , 2005, Journal of Molecular Evolution.

[32]  Burkhard Morgenstern,et al.  DIALIGN: multiple DNA and protein sequence alignment at BiBiServ , 2004, Nucleic Acids Res..

[33]  R Leplae,et al.  Analysis and assessment of comparative modeling predictions in CASP4 , 2001, Proteins.

[34]  J. L. Jensen,et al.  Probabilistic models of DNA sequence evolution with context dependent rates of substitution , 2000, Advances in Applied Probability.

[35]  Jens Stoye,et al.  Benchmarking tools for the alignment of functional noncoding DNA , 2004, BMC Bioinformatics.

[36]  Michael S. Waterman,et al.  Technical Note - Determining All Optimal and Near-Optimal Solutions when Solving Shortest Path Problems by Dynamic Programming , 1984, Oper. Res..

[37]  E. Lander,et al.  Parametric sequence comparisons. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[38]  P. Green,et al.  Transcription-associated mutational asymmetry in mammalian evolution , 2003, Nature Genetics.

[39]  Hongkai Ji,et al.  Why do human diversity levels vary at a megabase scale? , 2005, Genome research.

[40]  Burkhard Morgenstern,et al.  DIALIGN2: Improvement of the segment to segment approach to multiple sequence alignment , 1999, German Conference on Bioinformatics.

[41]  M S Waterman,et al.  Sequence alignments in the neighborhood of the optimum with general application to dynamic programming. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[42]  L. Duret,et al.  Recombination drives the evolution of GC-content in the human genome. , 2004, Molecular biology and evolution.

[43]  D. Haussler,et al.  Human-mouse alignments with BLASTZ. , 2003, Genome research.

[44]  Inna Dubchak,et al.  Automated whole-genome multiple alignment of rat, mouse, and human. , 2004, Genome research.

[45]  Francesca Chiaromonte,et al.  Scoring Pairwise Genomic Sequence Alignments , 2001, Pacific Symposium on Biocomputing.

[46]  István Miklós,et al.  Bayesian coestimation of phylogeny and sequence alignment , 2005, BMC Bioinformatics.

[47]  Serafim Batzoglou,et al.  The many faces of sequence alignment , 2005, Briefings Bioinform..

[48]  Dirk Metzler,et al.  Statistical alignment based on fragment insertion and deletion models , 2003, Bioinform..

[49]  Maximilian Schlosshauer,et al.  A novel approach to local reliability of sequence alignments , 2002, Bioinform..

[50]  Colin N. Dewey,et al.  Initial sequencing and comparative analysis of the mouse genome. , 2002 .

[51]  T. Speed,et al.  Biological Sequence Analysis , 1998 .

[52]  Ian Holmes,et al.  Dynamic Programming Alignment Accuracy , 1998, J. Comput. Biol..

[53]  P. Green,et al.  Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[54]  Erik L. L. Sonnhammer,et al.  An HMM posterior decoder for sequence feature prediction that includes homology information , 2005, ISMB.

[55]  Ian Holmes,et al.  Dynamic programming alignment accuracy , 1998, RECOMB '98.

[56]  P H Sellers.  Pattern recognition in genetic sequences. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[57]  M. Vingron,et al.  Quantifying the local reliability of a sequence alignment. , 1996, Protein engineering.

[58]  Jeremy Buhler,et al.  Choosing the best heuristic for seeded alignment of DNA sequences , 2006, BMC Bioinformatics.

[59]  Dan Gusfield,et al.  Parametric optimization of sequence alignment , 1992, SODA '92.

[60]  D. Petrov,et al.  A Novel Method Distinguishes Between Mutation Rates and Fixation Biases in Patterns of Single-Nucleotide Substitution , 2006, Journal of Molecular Evolution.

[61]  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.

[62]  Chuong B. Do,et al.  ProbCons: Probabilistic consistency-based multiple sequence alignment. , 2005, Genome research.

[63]  Robert C. Edgar,et al.  Multiple sequence alignment. , 2006, Current opinion in structural biology.

[64]  Lior Pachter,et al.  Parametric Alignment of Drosophila Genomes , 2005, PLoS Comput. Biol..

[65]  J. Felsenstein,et al.  An evolutionary model for maximum likelihood alignment of DNA sequences , 1991, Journal of Molecular Evolution.

[66]  A. Prakash,et al.  Measuring the accuracy of genome-size multiple alignments , 2007, Genome Biology.