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Activity Number:
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141
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Type:
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Topic Contributed
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Date/Time:
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Monday, July 30, 2007 : 10:30 AM to 12:30 PM
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Sponsor:
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IMS
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| Abstract - #309742 |
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Title:
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Spatial Location-Dependent Substitution Models and Their Application to Phylogenetics
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Author(s):
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Xueliang Pan*+ and Dennis K. Pearl and J. Dennis Pollack
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Companies:
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The Ohio State University and The Ohio State University and The Ohio State University
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Address:
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3536 Chowning Ct, Columbus, OH, 43220,
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Keywords:
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phylogeny ; Bayesian method ; substitution model ; crystallography
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Abstract:
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The conservation of the amino acids in homologous DNA sequences depends on a selection process that depends on functional and structural constraints. In this study, a model allowing site variation (conservation) to depend on spatial location is presented to reconstruct the phylogeny using Markov Chain Monte Carlo methods. The spatial location of each amino acid is obtained independently from crystallographic images. The model then assumes that conservation is monotonically increasing as we get closer in space to the functional core of a protein. Differences in quality of fit, in convergence and computational efficiency between this model and some other widely used models allowing rate variation are compared. We demonstrate the usefulness of the model by analyzing large data sets with sequences from 12 different enzymes which are each found in species from all Kingdoms.
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