Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi

(2013) Daniel L. Lindner et al.   Ecology and Evolution

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets

(2012) Johan Bengtsson et al.   RESEARCH IN MICROBIOLOGY

Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

(2011) Johan Bengtsson et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Recent developments in the taxonomic affiliation and phylogenetic positioning of fungi: impact in applied microbiology and environmental biotechnology

(2011) Kerstin Voigt et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

V-REVCOMP: automated high-throughput detection of reverse complementary 16S rRNA gene sequences in large environmental and taxonomic datasets

(2011) Martin Hartmann et al.   FEMS MICROBIOLOGY LETTERS

Molecular techniques revolutionize knowledge of basidiomycete evolution

(2011) Zhu L. Yang   FUNGAL DIVERSITY

A Consistent Phylogenetic Backbone for the Fungi

(2011) I. Ebersberger et al.   MOLECULAR BIOLOGY AND EVOLUTION

High consistency between replicate 454 pyrosequencing analyses of ectomycorrhizal plant root samples

(2011) Håvard Kauserud et al.   MYCORRHIZA

Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants

(2011) et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences

(2011) David S. Hibbett et al.   Fungal Biology Reviews

Post-genomic approaches to understanding interactions between fungi and their environment

(2011) Ronald P. De Vries et al.   IMA Fungus

Current state and perspectives of fungal DNA barcoding and rapid identification procedures

(2010) Dominik Begerow et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

(2010) Eva Bellemain et al.   BMC MICROBIOLOGY

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

(2010) R. Henrik Nilsson et al.   Fungal Ecology

V-Xtractor: An open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences

(2010) Martin Hartmann et al.   JOURNAL OF MICROBIOLOGICAL METHODS

An open source chimera checker for the fungal ITS region

(2010) R. H. NILSSON et al.   Molecular Ecology Resources

A note on the incidence of reverse complementary fungal ITS sequences in the public sequence databases and a software tool for their detection and reorientation

(2010) R. Henrik Nilsson et al.   MYCOSCIENCE

A constructive step towards selecting a DNA barcode for fungi

(2010) Ursula Eberhardt   NEW PHYTOLOGIST

Insidious effects of sequencing errors on perceived diversity in molecular surveys

(2010) Ian A. Dickie   NEW PHYTOLOGIST

454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases

(2010) Leho Tedersoo et al.   NEW PHYTOLOGIST

The International Nucleotide Sequence Database Collaboration

(2010) G. Cochrane et al.   NUCLEIC ACIDS RESEARCH

The Promise and Pitfalls of Sequence-Based Identification of Plant-Pathogenic Fungi and Oomycetes

(2010) Seogchan Kang et al.   PHYTOPATHOLOGY

The ITS region as a target for characterization of fungal communities using emerging sequencing technologies

(2009) Rolf Henrik Nilsson et al.   FEMS MICROBIOLOGY LETTERS

Progress towards DNA barcoding of fungi

(2009) KEITH A. SEIFERT   Molecular Ecology Resources

Fungal ecology catches fire

(2009) David S. Hibbett et al.   NEW PHYTOLOGIST

The ITS2 Database III—sequences and structures for phylogeny

(2009) Christian Koetschan et al.   NUCLEIC ACIDS RESEARCH

Fungal Community Ecology: A Hybrid Beast with a Molecular Master

(2008) Kabir G. Peay et al.   BIOSCIENCE

5.8S-28S rRNA interaction and HMM-based ITS2 annotation

(2008) Alexander Keller et al.   GENE

Internal transcribed spacer primers and sequences for improved characterization of basidiomycetous orchid mycorrhizas

(2008) D. Lee Taylor et al.   NEW PHYTOLOGIST