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

作者：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; Koljalg Urmas; Abarenkov Kessy

来源：Mycoscience, 2011, 52(4): 278-282.

DOI：10.1007/s10267-010-0086-z

• DNA barcoding
• Environmental sampling
• Hidden Markov models
• Quality assessment
• Sequence identification

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.

• 出版日期2011-7