title: jMOTU and Taxonerator: turning DNA Barcode sequences into annotated operational taxonomic units.
abstract: BACKGROUND
  DNA barcoding and other DNA sequence-based techniques for investigating and estimating biodiversity require explicit methods for associating individual sequences with taxa, as it is at the taxon level that biodiversity is assessed. For many projects, the bioinformatic analyses required pose problems for laboratories whose prime expertise is not in bioinformatics. User-friendly tools are required for both clustering sequences into molecular operational taxonomic units (MOTU) and for associating these MOTU with known organismal taxonomies.
  
  
  RESULTS
  Here we present jMOTU, a Java program for the analysis of DNA barcode datasets that uses an explicit, determinate algorithm to define MOTU. We demonstrate its usefulness for both individual specimen-based Sanger sequencing surveys and bulk-environment metagenetic surveys using long-read next-generation sequencing data. jMOTU is driven through a graphical user interface, and can analyse tens of thousands of sequences in a short time on a desktop computer. A companion program, Taxonerator, that adds traditional taxonomic annotation to MOTU, is also presented. Clustering and taxonomic annotation data are stored in a relational database, and are thus amenable to subsequent data mining and web presentation.
  
  
  CONCLUSIONS
  jMOTU efficiently and robustly identifies the molecular taxa present in survey datasets, and Taxonerator decorates the MOTU with putative identifications. jMOTU and Taxonerator are freely available from http://www.nematodes.org/.
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: Martin
authors.initials: M
authors.lastname: Jones
authors.forename: Anisah
authors.initials: A
authors.lastname: Ghoorah
authors.forename: Mark
authors.initials: M
authors.lastname: Blaxter
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D001493:Bathing Beaches; D044822:Biodiversity; D002080:Butterflies / Q000235:genetics; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D017753:Ecosystem; D003576:Electron Transport Complex IV / Q000235:genetics; D058977:Molecular Sequence Annotation / Q000379:methods*; D012335:RNA, Ribosomal / Q000235:genetics; D054679:Ribosome Subunits, Small / Q000235:genetics; D012606:Scotland; D017422:Sequence Analysis, DNA
chemical_list: D012335:RNA, Ribosomal; D003576:Electron Transport Complex IV