We have developed methods for molecular species identification, more specifically probabilistic methods for taxonomic placement (PROTAX) of DNA barcoding sequences. What makes PROTAX different from the broad variety of other kinds of bioinformatics methods is that it is based on a statistically rigorous approach, allowing the unbiased assessment of species identification uncertainty.

To exemplify the output of PROTAX, the interactive wheel shows wood-inhabiting fungi that we identified from DNA extracted from a saw dust sample drilled from a Norwegian spruce log. The areas of the sectors show the fraction of sequences identified to each unit. If selecting “color by confidence”, the pink color (confidence level 6) shows those identifications about which we can be most certain about: with these, the probability of correct identification is at least 90%.

The PROTAX software

PROTAX output example

Key publications:
Somervuo, P., Koskela, S., Pennanen, J., Nilsson, H. and Ovaskainen, O. 2016. Unbiased probabilistic taxonomic classification for DNA barcoding. Bioinformatics, in press.