Specificity, Sensitivity and Enrichment Ratios for validation sets across all phenotypes: (A) Known disease genes validation set and (B) WTCCC candidate genes validation set for alternate SNP/gene approaches across all thresholds. Light blue depicts CPS seeded, dark blue-CPS ab initio, yellow-CMP seeded and red-CMP ab initio. On the primary axis, specificity is shown by shaded boxes and sensitivity by open boxes. On the secondary axis the enrichment ratios are shown as lines. For CPS, the sensitivity increased for the NN sets (adjacent, nearest and resident). For CMP, the sensitivity was low due to few predictions. For CPS and CMP, specificity decreased for the NN sets. The enrichment ratios decreased for CPS seeded for the NN sets, while for CPS ab initio, the highest enrichment ratio was for the 0.5 Mbp BY search space constructed from the WS SNP set, the 0.1 Mbp BY for the MWS and MHS sets, and the adjacent NN for the HS set. Some values are obscured, but have been listed in the supplementary Table S2 (Additional file 1).