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Abstract Details
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Activity Number:
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224
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Type:
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Topic Contributed
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Date/Time:
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Monday, July 30, 2012 : 2:00 PM to 3:50 PM
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Sponsor:
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Section on Statistical Computing
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| Abstract - #305414 |
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Title:
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Alignment-Free Genome and Metagenome Comparison Using K-Tuples
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Author(s):
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Fengzhu Sun*+
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Companies:
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University of Southern California
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Address:
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Molecular & Computational Biology Prg, Los Angeles, CA, 90089, United States
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Keywords:
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alignment-free ;
metagenomics comparison ;
genome comparison ;
k-tuple ;
limit distribution ;
Markov model
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Abstract:
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Next generation sequencing (NGS) technologies have generated enormous amount of shotgun read data and assembly of the reads can be challenging, especially for organisms without template sequences. We develop novel alignment-free and assemble-free statistics for genome and metagenome comparison and study their limit behaviors. The statistics were used to study the evolutionary relationships among 13 tree species whose templates sequences are not known. They were also used to classify metagenomes from mammalian species, global ocean survey, and human gut. In both applications, our novel statistics yield clustering that is consistent with biological knowledge. Thus, our statistics provide a powerful alternative approach for genome and metagenome comparison based on NGS short reads.
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The address information is for the authors that have a + after their name.
Authors who are presenting talks have a * after their name.
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