Clustering metagenomic sequences with interpolated Markov models |
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Authors: | David R Kelley Steven L Salzberg |
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Institution: | 1.Center for Bioinformatics and Computational Biology,Institute for Advanced Computer Studies,College Park,USA;2.Department of Computer Science,University of Maryland,USA |
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Abstract: | Background Sequencing of environmental DNA (often called metagenomics) has shown tremendous potential to uncover the vast number of unknown
microbes that cannot be cultured and sequenced by traditional methods. Because the output from metagenomic sequencing is a
large set of reads of unknown origin, clustering reads together that were sequenced from the same species is a crucial analysis
step. Many effective approaches to this task rely on sequenced genomes in public databases, but these genomes are a highly
biased sample that is not necessarily representative of environments interesting to many metagenomics projects. |
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