Endelman BMC Genomics 2011, 12:407 http://www.biomedcentral.com/1471-2164/12/407 Page 8 of 9 Figure 3 Consensus maps of the barley 5HS telomere. The rescaled consensus maps from DAGGER and MergeMap (distances in cM) are shown alongside a physical map of the hardness locus. The scale of the physical map relative to the consensus maps is arbitrary; the scale bar refers only to the physical map. The consensus map produced by DAGGER is generated by linearizing an unsimplified consensus graph that is equivalent to the linkage maps. By contrast, the consensus map produced by MergeMap is generated by linearizing a simplified consensus graph that is consistent with but not equivalent to the linkage maps. Based on the linkage maps in Table 2, the hardness locus should be less than 1 cM in length; this is true in the DAGGER map but not the consensus map from MergeMap. Statistical analysis was conducted using PROC MIXED in SAS 9.2 (SAS Institute, Cary, NC), with each simulation as “subject” to properly model the covariance structure (LP and QP consensus maps were generated for each simulation). Figure 4 RMS error between the consensus map and barley linkage maps. The SNP consensus map from DAGGER had consistently less error than the consensus map from MergeMap. When averaged over the seven chromosomes, the RMS error (square root of normalized Equation 1) was 0.82 cM per marker interval with DAGGER compared to 2.28 cM with MergeMap. Validation with barley data When the four linkage maps published by Close et al. [11] were used as input for DAGGER, no ordering conflicts were detected. Markers from unassigned linkage groups were not included, which led to three fewer markers (3_0024, 3_0764, 2_1056) in the consensus map of chro- mosome 4H compared with the results of Close et al. [11]. The DAGGER consensus map for each chromosome took several seconds to generate on a laptop computer running R 2.12.1 [22]. Following the procedure of Close et al. [11], the consensus maps were rescaled (by chromosome) to equal the mean length of the four linkage maps. Comparisons were made to both the published results of Close et al. [11] as well as de novo results generated by submitting the four linkage maps to MergeMap Online [16] on 23 Feb. 2011 (followed by rescaling). The comparisons were nearly identical, e.g., the RMS error for the map of Close et al. [11] was 2.23 cM vs. 2.28 cM for the de novo MergeMap output. The results in this manuscript are for the de novo MergeMap output. The physical map in Figure 3 is based on GenBank accession number AH014393.1[21]. The positions of the SNP markers on the physical map were determined using BLAST 2 Sequences [30], with the query sequences taken from Close et al. [11]. The consensus map illustrations in Figure 3 were created using Map- Chart [31].