An open source chimera checker for the fungal ITS region
Journal article, 2010

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.


chimeric sequences

environmental sampling

internal transcribed spacer


R. Henrik Nilsson

University of Gothenburg

Kessy Abarenkov

Vilmar Veldre

Stephan Nylinder

University of Gothenburg

Pierre De Wit

University of Gothenburg

Sara Brosché

University of Gothenburg

Johan F. Alfredsson

Martin Ryberg

Erik Kristiansson

University of Gothenburg

Molecular Ecology Resources

1755-098X (ISSN) 1755-0998 (eISSN)

Vol. 10 6 1076-1081

Subject Categories

Biological Systematics



Bioinformatics and Systems Biology



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