Encyclopedia of Metagenomics

Living Edition
| Editors: Karen E. Nelson

Metaxa, Overview

  • Johan Bengtsson-Palme
  • Martin Hartmann
  • K. Martin Eriksson
  • R Henrik Nilsson
Living reference work entry
DOI: https://doi.org/10.1007/978-1-4614-6418-1_239-6

Synonyms

Definition

Metaxa is a software tool for extracting full-length and partial ribosomal small subunit (SSU; 16S/18S/12S) sequences from metagenomic datasets and for classifying the extracted sequences to taxonomic domains and organelle of origin. Metaxa is freely available from http://microbiology.se/software/metaxa/.

Introduction

A common question in metagenomic studies concerns the species composition of the community sampled (Desai et al. 2012). This is frequently addressed using a specific genetic marker, typically the ribosomal RNA (rRNA) small subunit (SSU) gene sequence (also referred to as the 16S, 18S, or 12S subunit depending on the lineage under scrutiny). In some studies, the SSU gene is amplified by PCR and sequenced separately in order to study microbial diversity. However, even if the SSU sequences are not targeted for separate sequencing, it is still possible to identify and extract the SSU...

Keywords

FASTA File Metagenomic Dataset Blast Match Silva Database Taxonomic Domain 
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 2014

Authors and Affiliations

  • Johan Bengtsson-Palme
    • 1
  • Martin Hartmann
    • 2
  • K. Martin Eriksson
    • 3
  • R Henrik Nilsson
    • 3
  1. 1.Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of GothenburgGöteborgSweden
  2. 2.Molecular Ecology, Agroscope Reckenholz-Tänikon Research Station ARTZurichSwitzerland
  3. 3.Department of Biological and Environmental SciencesUniversity of GothenburgGöteborgSweden