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
Artikel i vetenskaplig tidskrift, 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

Författare

R. Henrik Nilsson

Göteborgs universitet

Vilmar Veldre

Martin Eckart

Sara Branco

Martin Hartmann

Christopher Quince

Anna Godhe

Göteborgs universitet

Yann Bertrand

Göteborgs universitet

Johan F. Alfredsson

Karl-Henrik Larsson

Göteborgs universitet

Urmas Kõljalg

Kessy Abarenkov

Mycoscience

1340-3540 (ISSN) 1618-2545 (eISSN)

Vol. 52 278-282

Ämneskategorier

Biologisk systematik

Ekologi

Annan biologi

Bioinformatik och systembiologi

DOI

10.1007/s10267-010-0086-z