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

Nilsson, R. Henrik, Veldre, Vilmar, Wang, Zheng, Eckart, Martin, Branco, Sara, Hartmann, Martin, Quince, Christopher, Godhe, Anna, Bertrand, Yann, Alfredsson, Johan F., Larsson, Karl Henrik, Kõljalg, Urmas and Abarenkov, Kessy (2011) 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. Mycoscience, 52 (4). pp. 278-282. ISSN 1340-3540

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Abstract

Reverse complementary DNA sequences--sequences that are inadvertently cast backward and in which all purines and pyrimidines are transposed--are not uncommon in sequence databases, where they may introduce noise into sequence-based research. We show that about 1% of the public fungal ITS sequences, the most commonly sequenced genetic marker in mycology, are reverse complementary, and we introduce an open source software solution to automate their detection and reorientation. The MacOSX/Linux/UNIX software operates on public or private datasets of any size, although some 50 base pairs of the 5.8S gene of the ITS region are needed for the analysis.

Item Type: Article
Additional Information: Funding Information: Acknowledgments R.H.N. and K.A. gratefully acknowledge support from the Frontiers in Biodiversity Research Centre of Excellence (University of Tartu) and the Fungi in Boreal Forest Soils network. Matt von Konrat and Anders Hagborg are acknowledged for valuable advice on the liverwort data. Two anonymous reviewers are acknowledged for valuable input on the manuscript. The authors declare that they have no conflict of interests. No laboratory experiments were undertaken as a component––or result––of the present study.
Uncontrolled Keywords: dna barcoding,environmental sampling,hidden markov models,quality assessment,sequence identification,ecology, evolution, behavior and systematics ,/dk/atira/pure/subjectarea/asjc/1100/1105
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 12 Sep 2022 10:32
Last Modified: 23 Sep 2022 02:53
URI: https://ueaeprints.uea.ac.uk/id/eprint/88119
DOI: 10.1007/s10267-010-0086-z

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