Encyclopedia of Metagenomics

Living Edition
| Editors: Karen E. Nelson

Taxonomic Classification of Metagenomic Shotgun Sequences with CARMA3

Living reference work entry
DOI: https://doi.org/10.1007/978-1-4614-6418-1_751-2

Synonyms

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...

Keywords

Taxonomic Classification Taxonomic Rank Metagenomic Sequence Lower Common Ancestor Lower Common Ancestor 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.Institute for Genomics and Systems BiologyArgonne National LaboratoryArgonneUSA
  2. 2.Faculty of TechnologyBielefeld UniversityBielefeldGermany