CPL - Chalmers Publication Library
| Utbildning | Forskning | Styrkeområden | Om Chalmers | In English In English Ej inloggad.

An open source chimera checker for the fungal ITS region

R. Henrik Nilsson ; Vilmar Veldre ; Kessy Abarenkov ; Stephan Nylinder ; Pierre De Wit ; Sara Brosché ; Johan Alfredsson ; Martin Ryberg ; Erik Kristiansson (Institutionen för neurovetenskap och fysiologi ; Zoologiska institutionen, zoofysiologi ; Zoologiska institutionen ; Institutionen för matematiska vetenskaper, matematisk statistik)
9th International Mycological Congress, Edinburgh, UK (2010)
[Konferensbidrag, poster]

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 http://www.emerencia.org/chimerachecker.html) 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.

Nyckelord: Chimera checker, ITS, sequence analysis

Denna post skapades 2010-08-11. Senast ändrad 2011-01-20.
CPL Pubid: 124372


Institutioner (Chalmers)

Institutionen för växt- och miljövetenskaper (2006-2011)
Zoologiska institutionen (1954-2011)
Institutionen för neurovetenskap och fysiologi (GU)
Zoologiska institutionen, zoofysiologi (1988-2011)
Institutionen för matematiska vetenskaper, matematisk statistik (2005-2016)


Bioinformatik och systembiologi
Terrestrisk ekologi
Biologisk systematik

Chalmers infrastruktur