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FORMAL: A model to identify organisms present in metagenomes using Monte Carlo Simulation

Genivaldo Gueiros Z. Silva, Bas E. Dutilh, Robert A. Edwards
doi: https://doi.org/10.1101/010801
Genivaldo Gueiros Z. Silva
1Computational Science Research Center, 5500 Campanile Drive, San Diego, CA 92182, USA
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Bas E. Dutilh
4Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
5Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Brazil
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Robert A. Edwards
1Computational Science Research Center, 5500 Campanile Drive, San Diego, CA 92182, USA
2Department of Computer Science, 5500 Campanile Drive, San Diego, CA 92182, USA
3Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
5Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Brazil
6Division of Mathematics and Computer Science, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439, USA
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  • For correspondence: redwards@mail.sdsu.edu
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Abstract

One of the major goals in metagenomics is to identify organisms present in the microbial community from a huge set of unknown DNA sequences. This profiling has valuable applications in multiple important areas of medical research such as disease diagnostics. Nevertheless, it is not a simple task, and many approaches that have been developed are slow and depend on the read length of the DNA sequences. Here we introduce an innovative and agile approach which k-mer and Monte Carlo simulation to profile and report abundant organisms present in metagenomic samples and their relative abundance without sequence length dependencies. The program was tested with a simulated metagenomes, and the results show that our approach predicts the organisms in microbial communities and their relative abundance.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 28, 2014.
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FORMAL: A model to identify organisms present in metagenomes using Monte Carlo Simulation
Genivaldo Gueiros Z. Silva, Bas E. Dutilh, Robert A. Edwards
bioRxiv 010801; doi: https://doi.org/10.1101/010801
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FORMAL: A model to identify organisms present in metagenomes using Monte Carlo Simulation
Genivaldo Gueiros Z. Silva, Bas E. Dutilh, Robert A. Edwards
bioRxiv 010801; doi: https://doi.org/10.1101/010801

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