Ophir et al. BMC Genomics 2010, 11:269 http://www.biomedcentral.com/1471-2164/11/269 Page 6 of 10 Figure 3 Distribution of SFPs per gene. The number of SFPs per Uni- Gene (EST contig) was counted and the frequencies were plotted as a bar plot. Numbers above the columns are the percentage of gene counts in each category out of total counts. transcriptome, flexibility in format design and lower price. We anticipate that by improving the array design and adding the complementary strand for each probe, the FDR will be reduced as suggested by Smemo et al [37]. As the new Agilent and Nimblgen platforms hold much larger probes sets, one can increase the number of probes for any given sequence without hampering coverage. Another solution is increasing the statistical threshold in order to the decrease the FDR. There no doubt that this approach will reduced the discrepancy in FDR but will also will reduced dramaticly the number of SFPs that are discovered [34]. The question of conservation of the SFP markers across melon cultivars was tested using two different mapping populations (Figures 5 and 6). The data presented here show that a large portion of the SFPs are conserved between the different populations. This experiment dem- onstrated another advantage of SFP technology, which utilizes large sets of probes with no assumption of the location of the changes in different mapping populations. Figure 4 Number of SFPs per gene is not correlated with UniGene contig length. Box plots of UniGene contig length for each SFP/gene catego- ry. The length of the original contig from which the probes were designed. Descriptive statistics of UniGene length for each SFP/gene category were calculated. Medians of UniGene lengths are represented by horizontal thick lines in the boxes and box borders represent the 25th and 75th percen- tiles. Medians are approximately the same for all categories.