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Encyclopedia of Metagenomics pp 1–8Cite as

Taxonomic Classification of Metagenomic Shotgun Sequences with CARMA3

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Synonyms

Classification; Metagenome; Taxonomy

Definition

CARMA3 is a program to assign taxonomic identifiers to metagenomic sequences of unknown taxonomic origin.

Introduction

The vast majority of microbes cannot be cultivated in a monoculture and thus cannot be sequenced by means of traditional methods. To explore these microbes, they have to be analyzed within their natural microbial communities. High-throughput sequencing (HTS) technologies like Roche’s 454 sequencing, ABI’s SOLiD, or Illumina’s Genome Analyzer make it possible to sequence microbial DNA samples of such communities, called metagenomes. Due to the restricted read lengths produced by these technologies, reconstruction of complete genomic sequences from a metagenome is impossible. However, by comparing the metagenomic fragments with sequences of known function, it is possible to analyze the biological diversity and the underlying metabolic pathways in microbial communities.

To infer the taxonomic origin of metagenomic...

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Author information

Authors and Affiliations

  1. Institute for Genomics and Systems Biology, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA

    Wolfgang Gerlach

  2. Faculty of Technology, Bielefeld University, Bielefeld, Germany

    Jens Stoye

Authors
  1. Wolfgang Gerlach
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  2. Jens Stoye
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Corresponding author

Correspondence to Wolfgang Gerlach .

Editor information

Editors and Affiliations

  1. J. Craig Venter Institute (JCVI), Rockville, Maryland, USA

    Karen E. Nelson

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© 2013 Springer Science+Business Media New York

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Gerlach, W., Stoye, J. (2013). Taxonomic Classification of Metagenomic Shotgun Sequences with CARMA3. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_751-2

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  • DOI: https://doi.org/10.1007/978-1-4614-6418-1_751-2

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  • Publisher Name: Springer, New York, NY

  • Online ISBN: 978-1-4614-6418-1

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