jMOTU and Taxonerator: turning DNA Barcode sequences into annotated operational taxonomic units |
| |
Authors: | Jones Martin Ghoorah Anisah Blaxter Mark |
| |
Institution: | Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom. |
| |
Abstract: | BackgroundDNA 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.ResultsHere 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.ConclusionsjMOTU 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/. |
| |
Keywords: | |
本文献已被 PubMed 等数据库收录! |
|