Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes
John A Lees, Minna Vehkala, Niko Välimäki, Simon R Harris, Claire Chewapreecha, Nicholas J Croucher, Pekka Marttinen, Mark R Davies, Andrew C Steer, Stephen Y C Tong, Antti Honkela, Julian Parkhill, Stephen D Bentley, Jukka Corander
This paper introduces SEER, a statistical method to identify sequence elements associated with bacterial phenotypes, demonstrating its application in discovering antibiotic resistance and invasiveness factors in Streptococcus species.
bioRxiv · Mar 2, 2016Genomics