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
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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.
KeywordsDNA barcoding Environmental sampling Hidden Markov models Quality assessment Sequence identification
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.
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