Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data-Reference-Cited by-同舟云学术

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

Published:2013-07 Issue: Volume: Page:n/a-n/a
ISSN:2041-210X
Container-title:Methods in Ecology and Evolution
language:en
Short-container-title:Methods Ecol Evol

Author:

Bengtsson-Palme Johan¹,Ryberg Martin²,Hartmann Martin,Branco Sara³,Wang Zheng⁴,Godhe Anna⁵,De Wit Pierre⁵,Sánchez-García Marisol⁶,Ebersberger Ingo⁷,de Sousa Filipe⁵,Amend Anthony S.⁸,Jumpponen Ari⁹,Unterseher Martin¹⁰,Kristiansson Erik¹¹,Abarenkov Kessy¹²,Bertrand Yann J. K.⁵,Sanli Kemal⁵,Eriksson K. Martin¹³,Vik Unni¹⁴,Veldre Vilmar,Nilsson R. Henrik⁵

Affiliation:

1. Department of Neuroscience and Physiology; The Sahlgrenska Academy; University of Gothenburg; Box 434; 40530; Göteborg; Sweden

2. Department of Organismal Biology; Uppsala University; Norbyvägen 18D; Uppsala; 75236; Sweden

3. Department of Plant and Microbial Biology; University of California; Berkeley; CA; 94720-3102; USA

4. Department of Ecology and Evolutionary Biology; Yale University; New Haven; CT 06520-8106; USA

5. Department of Biological and Environmental Sciences; University of Gothenburg; Box 461; Göteborg; 40530; Sweden

6. Department of Ecology and Evolutionary Biology; University of Tennessee; Knoxville; TN; 37996-1610; USA

7. Department for Applied Bioinformatics; Institute for Cell Biology and Neuroscience, Goethe University; Max-von-Laue Str. 13; Frankfurt; D-60438; Germany

8. Botany Department; University of Hawai'i at Manoa; 3190 Maile Way; Honolulu; HI; 96822; USA

9. Division of Biology; Kansas State University; Manhattan; KS; 66506; USA

10. Institute of Botany and Landscape Ecology; Ernst-Moritz-Arndt University Greifswald; Grimmer Str. 88; Greifswald; D-17487; Germany

11. Department of Mathematical Statistics; Chalmers University of Technology; Göteborg; 41296; Sweden

12. Natural History Museum; University of Tartu; 46 Vanemuise Str.; Tartu; 51014; Estonia

13. Department of Shipping and Marine Technology; Chalmers University of Technology; Göteborg; 41296; Sweden

14. Department of Biosciences; University of Oslo; PO Box 1066, Blindern; Oslo; N-0316; Norway

Publisher

Wiley

Subject

Ecological Modeling,Ecology, Evolution, Behavior and Systematics

Link

http://onlinelibrary.wiley.com/wol1/doi/10.1111/2041-210X.12073/fullpdf

Reference49 articles.

1. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs;Altschul;Nucleic Acids Research,1997

2. Current state and perspectives of fungal DNA barcoding and rapid identification procedures;Begerow;Applied Microbiology and Biotechnology,2010

3. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases;Bellemain;BMC Microbiology,2010

4. 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;Bengtsson;Antonie van Leeuwenhoek,2011

5. 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;Bengtsson;Research in Microbiology,2012

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