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
Artikel i vetenskaplig tidskrift, 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

Författare

R. Henrik Nilsson

Göteborgs universitet

Vilmar Veldre

Martin Hartmann

Martin Unterseher

Anthony Amend

Johannes Bergsten

Erik Kristiansson

Göteborgs universitet

Martin Ryberg

Ari Jumpponen

Kessy Abarenkov

Fungal Ecology

1754-5048 (ISSN)

Vol. 3 4 284-287

Ämneskategorier

Biologisk systematik

Markvetenskap

Ekologi

Mikrobiologi

Bioinformatik och systembiologi

DOI

10.1016/j.funeco.2010.05.002