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

R Henrik Nilsson,Martin Ryberg,Martin Hartmann,Vilmar Veldre,Ari Jumpponen,Anthony Amend,Kessy Abarenkov,Johannes Bergsten,Martin Unterseher,Erik Kristiansson

doi:10.1016/j.funeco.2010.05.002

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

R Henrik Nilsson, Martin Ryberg + Show 8 more

https://doi.org/10.1016/j.funeco.2010.05.002

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Journal: Fungal Ecology	Publication Date: Jun 30, 2010
Citations: 193

Affiliation: University of Tennessee at Knoxville, University of British Columbia, University of Tartu, Kansas State University, University of Gothenburg, University of California, Berkeley, Swedish Museum of Natural History, University of Greifswald

#Fungal ITS Sequences #Fungal ITS + Show 8 more

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Abstract

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.

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