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    JCB
    2007
    97views more  JCB 2007»
    Parsing Nucleic Acid Pseudoknotted Secondary Structure: Algorithm and Applications
    13 years 11 months ago
    Parsing Nucleic Acid Pseudoknotted Secondary Structure: Algorithm and Applications
    Download  www.cs.ubc.ca
    Accurate prediction of pseudoknotted nucleic acid secondary structure is an important computational challenge. Prediction algorithms based on dynamic programming aim to find a st...
    Baharak Rastegari, Anne Condon
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    JCB
    2007
    106views more  JCB 2007»
    Clustered Sequence Representation for Fast Homology Search
    13 years 11 months ago
    Clustered Sequence Representation for Fast Homology Search
    Download  web.udl.es
    We present a novel approach to managing redundancy in sequence databanks such as GenBank. We store clusters of near-identical sequences as a representative union-sequence and a se...
    Michael Cameron, Yaniv Bernstein, Hugh E. Williams
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    JCB
    2007
    198views more  JCB 2007»
    Bayesian Hierarchical Model for Large-Scale Covariance Matrix Estimation
    13 years 11 months ago
    Bayesian Hierarchical Model for Large-Scale Covariance Matrix Estimation
    Download  www.eecs.umich.edu
    Many bioinformatics problems can implicitly depend on estimating large-scale covariance matrix. The traditional approaches tend to give rise to high variance and low accuracy esti...
    Dongxiao Zhu, Alfred O. Hero III
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    JCB
    2007
    144views more  JCB 2007»
    Statistical Estimation of Statistical Mechanical Models: Helix-Coil Theory and Peptide Helicity Prediction
    13 years 11 months ago
    Statistical Estimation of Statistical Mechanical Models: Helix-Coil Theory and Peptide Helicity Prediction
    Download  www.stat.duke.edu
    Analysis of biopolymer sequences and structures generally adopts one of two approaches: use of detailed biophysical theoretical models of the system with experimentally-determined...
    Scott C. Schmidler, Joseph E. Lucas, Terrence G. O...
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    JCB
    2007
    168views more  JCB 2007»
    Fast Molecular Shape Matching Using Contact Maps
    13 years 11 months ago
    Fast Molecular Shape Matching Using Contact Maps
    Download  www.cse.ohio-state.edu
    In this paper, we study the problem of computing the similarity of two protein structures ring their contact-map overlap. Contact-map overlap abstracts the problem of computing th...
    Pankaj K. Agarwal, Nabil H. Mustafa, Yusu Wang
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    JCB
    2007
    107views more  JCB 2007»
    Effects of Long-Range Correlations in DNA on Sequence Alignment Score Statistics
    13 years 11 months ago
    Effects of Long-Range Correlations in DNA on Sequence Alignment Score Statistics
    Download  www.molgen.mpg.de
    Long-range correlations in genomic base composition are a ubiquitous statistical feature among many eukaryotic genomes. In this article, these correlations are shown to substantia...
    Philipp W. Messer, Ralf Bundschuh, Martin Vingron,...
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    JCB
    2007
    191views more  JCB 2007»
    Bayesian Haplotype Inference via the Dirichlet Process
    13 years 11 months ago
    Bayesian Haplotype Inference via the Dirichlet Process
    Download  www.cs.berkeley.edu
    The problem of inferring haplotypes from genotypes of single nucleotide polymorphisms (SNPs) is essential for the understanding of genetic variation within and among populations, ...
    Eric P. Xing, Michael I. Jordan, Roded Sharan
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    JCB
    2007
    94views more  JCB 2007»
    Locality and Gaps in RNA Comparison
    13 years 11 months ago
    Locality and Gaps in RNA Comparison
    Download  cs.haifa.ac.il
    Locality is an important and well-studied notion in comparative analysis of biological sequences. Similarly, taking into account affine gap penalties when calculating biological ...
    Rolf Backofen, Shihyen Chen, Danny Hermelin, Gad M...
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