A systematic search for discriminating sites in the 16S ribosomal RNA gene

Kristian Hovde Liland has co-authored a paper on variable selection in aligned 16S rRNA sequences together with Hilde Vinje, Trygve Almøy and Lars Snipen. The paper is titled: “A systematic search for discriminating sites in the 16S ribosomal RNA gene” and was recently published in the journal Microbial Informatics and Experimentation. This was the last paper to ever be accepted in the journal. Whether this was due to the journal editors feeling that the peak of their careers had been met with this paper and therefore decided to close the journal has not been confirmed.

Abstract

The 16S rRNA is by far the most common genomic marker used for prokaryotic classification, and has been used extensively in metagenomic studies over recent years. Along the 16S gene there are regions with more or less variation across the kingdom of bacteria. Nine variable regions have been identified, flanked by more conserved parts of the sequence. It has been stated that the discriminatory power of the 16S marker lies in these variable regions. In the present study we wanted to examine this more closely, and used a supervised learning method to search systematically for sites that contribute to correct classification at either the phylum or genus level.

Keywords

  • Partial least squares
  • Selectivity ratio
  • Sequence alignment
  • Entropy

Full citation

Hilde Vinje, Trygve Almøy, Kristian Hovde Liland, Lars Snipen,
A systematic search for discriminating sites in the 16S ribosomal RNA gene
Microbial Informatics and Experimentation 4(2) (2014).

DOI: 10.1186/2042-5783-4-2

http://dx.doi.org/10.1186/2042-5783-4-2