An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology
Journal article, 2010
We introduce an open source software utility to extract the highly variable ITS1 and ITS2 subregions from fungal nuclear ITS sequences, the region of choice for environmental sampling and molecular identification of fungi. Inclusion of parts of the neighbouring, very conserved, ribosomal genes in the sequence identification process regularly leads to distorted results. The utility is available for UNIX-type operating systems, including MacOS X, and processes about 1000 sequences per minute.
molecular ecology
sequence identification
environmental sampling
nuclear ribosomal genes
ITS
Author
R. Henrik Nilsson
University of Gothenburg
Vilmar Veldre
Martin Hartmann
Martin Unterseher
Anthony Amend
Johannes Bergsten
Erik Kristiansson
University of Gothenburg
Martin Ryberg
Ari Jumpponen
Kessy Abarenkov
Fungal Ecology
1754-5048 (ISSN)
Vol. 3 4 284-287Subject Categories
Biological Systematics
Soil Science
Ecology
Microbiology
Bioinformatics and Systems Biology
DOI
10.1016/j.funeco.2010.05.002