(Q57055810)

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

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

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Marisol Sánchez-García

object named as

Marisol Sánchez-García

8

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Kessy Abarenkov

object named as

Kessy Abarenkov

15

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Johan Bengtsson-Palme

object named as

Johan Bengtsson-Palme

1

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Rolf Henrik Nilsson

object named as

R. Henrik Nilsson

21

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Martin Hartmann

object named as

Martin Hartmann

3

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Martin Unterseher

13

object named as

Martin Unterseher

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2

object named as

Martin Ryberg

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object named as

Yann Bertrand

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Anthony S. Amend

11

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Anthony S. Amend

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6

object named as

Anna Godhe

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author name string

Sara Branco

4

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Zheng Wang

5

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Pierre De Wit

7

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Ingo Ebersberger

9

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Filipe de Sousa

10

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Ari Jumpponen

12

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Erik Kristiansson

14

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Kemal Sanli

17

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K. Martin Eriksson

18

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Unni Vik

19

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Vilmar Veldre

20

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publication date

July 2013

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Methods in Ecology and Evolution

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

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

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https://api.crossref.org/works/10.1111%2F2041-210X.12073

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

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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

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21 January 2018

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

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

The International Nucleotide Sequence Database Collaboration

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21 January 2018

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

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A constructive step towards selecting a DNA barcode for fungi

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A consistent phylogenetic backbone for the fungi

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Profile hidden Markov models

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21 January 2018

Accelerated Profile HMM Searches

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https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

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The magnitude of fungal diversity: the 1.5 million species estimate revisited

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Fungal ecology catches fire

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https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

Ribosomal DNA: Molecular Evolution and Phylogenetic Inference

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

The molecular revolution in ectomycorrhizal ecology: peeking into the black-box.

1 reference

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Reconstructing the early evolution of Fungi using a six-gene phylogeny

1 reference

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21 January 2018

The promise and pitfalls of sequence-based identification of plant-pathogenic fungi and oomycetes

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

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

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https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

The ITS2 Database III--sequences and structures for phylogeny

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https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

An open source chimera checker for the fungal ITS region

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

Improved tools for biological sequence comparison

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

Fungal Community Ecology: A Hybrid Beast with a Molecular Master

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

Removing noise from pyrosequenced amplicons

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

EMBOSS: the European Molecular Biology Open Software Suite

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

Progress towards DNA barcoding of fungi

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1111%2F2041-210X.12073

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

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https://api.crossref.org/works/10.1111%2F2041-210X.12073

21 January 2018

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

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21 January 2018

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10.1111/2041-210X.12073

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