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    BMCBI
    2008
    86views more  BMCBI 2008»
    Predicting protein linkages in bacteria: Which method is best depends on task
    13 years 5 months ago
    Predicting protein linkages in bacteria: Which method is best depends on task
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    Background: Applications of computational methods for predicting protein functional linkages are increasing. In recent years, several bacteria-specific methods for predicting link...
    Anis Karimpour-Fard, Sonia M. Leach, Ryan T. Gill,...
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    BMCBI
    2006
    128views more  BMCBI 2006»
    Comparative assessment of performance and genome dependence among phylogenetic profiling methods
    13 years 5 months ago
    Comparative assessment of performance and genome dependence among phylogenetic profiling methods
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    Background: The rapidly increasing speed with which genome sequence data can be generated will be accompanied by an exponential increase in the number of sequenced eukaryotes. Wit...
    Evan S. Snitkin, Adam M. Gustafson, Joseph C. Mell...
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    BMCBI
    2008
    130views more  BMCBI 2008»
    A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm
    13 years 5 months ago
    A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm
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    Background: The process of horizontal gene transfer (HGT) is believed to be widespread in Bacteria and Archaea, but little comparative data is available addressing its occurrence ...
    Sheila Podell, Terry Gaasterland, Eric E. Allen
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    BMCBI
    2007
    131views more  BMCBI 2007»
    On the detection of functionally coherent groups of protein domains with an extension to protein annotation
    13 years 5 months ago
    On the detection of functionally coherent groups of protein domains with an extension to protein annotation
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    Background: Protein domains coordinate to perform multifaceted cellular functions, and domain combinations serve as the functional building blocks of the cell. The available metho...
    William A. McLaughlin, Ken Chen, Tingjun Hou, Wei ...
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    BIBE
    2005
    IEEE
    88views Bioinformatics» more  BIBE 2005»
    Improved Phylogenetic Motif Detection Using Parsimony
    13 years 11 months ago
    Improved Phylogenetic Motif Detection Using Parsimony
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    We have recently demonstrated (La et al, Proteins, 58:2005) that sequence fragments approximating the overall familial phylogeny, called phylogenetic motifs (PMs), represent a pro...
    Usman Roshan, Dennis R. Livesay, David La
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