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An open source chimera checker for the fungal ITS region

Authors R. Henrik Nilsson
Vilmar Veldre
Kessy Abarenkov
Stephan Nylinder
Pierre De Wit
Sara Brosché
Johan Alfredsson
Martin Ryberg
Erik Kristiansson
Published in 9th International Mycological Congress, Edinburgh, UK
Publication year 2010
Published at Department of Plant and Environmental Sciences
Institute of Neuroscience and Physiology
Department of Mathematical Sciences, Mathematical Statistics
Department of Zoology
Department of Zoology, Zoophysiology
Language en
Keywords Chimera checker, ITS, sequence analysis
Subject categories Microbiology, Bioinformatics and Systems Biology, Terrestrial ecology, Biological Systematics


The internal transcribed spacer (ITS) region of the nuclear ribosomal repeat unit holds a central position in the pursuit of the taxonomic affiliation of fungi recovered through environmental sampling. Newly generated fungal ITS sequences are typically compared against the International Nucleotide Sequence Databases for a species or genus name using the sequence similarity software suite blast. Such searches are not without complications however, and one of them is the presence of chimeric entries among the query or reference sequences. Chimeras are artificial sequences, generated unintentionally during the polymerase chain reaction step, that feature sequence data from two (or possibly more) distinct species. Available software solutions for chimera control do not readily target the fungal ITS region, but the present study introduces a blast-based open source software package (available at to examine newly generated fungal ITS sequences for the presence of potentially chimeric elements in batch mode. We used the software package on a random set of 12 300 environmental fungal ITS sequences in the public sequence databases and found 1.5% of the entries to be chimeric at the ordinal level after manual verification of the results. The proportion of chimeras in the sequence databases can be hypothesized to increase as emerging sequencing technologies drawing from pooled DNA samples are becoming important tools in molecular ecology research.

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