Building MetaPhyler classifier To build MetaPhyler for a particular phylogenetic marker gene G and for length 60bp, we first simulate metagenomic reads from all reference marker genes, and as a negative set, from genomic sequences that do not contain marker genes. We then map these simulated reads against reference gene G using BLASTX. To build a classifier for gene G at a specific taxonomic level, say order, in vector Border we store BLASTX bit scores between gene G and the simulated reads that are from the same order; in vector Belse we store bit scores for aligning all other reads against G. We then find the bit score cutoff bcut that minimizes Equation 1. Finally, we repeat the previous steps to find bit score cutoffs for simulated reads of other lengths and for other genes.
Liu et al. BMC Genomics 2011 12(Suppl 2):S4 doi:10.1186/1471-2164-12-S2-S4