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
Journal article, 2011
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.
DNA barcoding - Environmental sampling - Hidden Markov models - Quality assessment - Sequence identification
Author
R. Henrik Nilsson
University of Gothenburg
Vilmar Veldre
Zheng Wang
Martin Eckart
Sara Branco
Martin Hartmann
Christopher Quince
Anna Godhe
University of Gothenburg
Yann Bertrand
University of Gothenburg
Johan F. Alfredsson
Karl-Henrik Larsson
University of Gothenburg
Urmas Kõljalg
Kessy Abarenkov
Mycoscience
1340-3540 (ISSN) 1618-2545 (eISSN)
Vol. 52 4 278-282Subject Categories
Biological Systematics
Ecology
Other Biological Topics
Bioinformatics and Systems Biology
DOI
10.1007/s10267-010-0086-z