Ophir et al. BMC Genomics 2010, 11:269 http://www.biomedcentral.com/1471-2164/11/269 lyzed and compared to the database sequence that was used as a reference. Additional material Additional file 1 List of 245 positive SFPs and their genotyping. The table describes the validation by Sanger sequencing and the difference, where there is one, between the probe and targets. Header descriptions. ProbeName - Probe index. Target - Target resource index as in the melon database v2 http://www.icugi.org/. Sequnce - probe sequence. Position - position of genetic variation within probe sequence. SFP - Either 1 for true positive (TP) or 0 for false positive (FP). NoSNP - number of single-nucle- otide polymorphisms (SNPs) in the SFP; 999 indicates many. IndelLength - Indel length if one exists. Pi - PI414723 genotype. Dulce - 'Dulce' genotype. Ref - probe genotype. t - the moderated-t statistic. logFC - log2 of PI-to- 'Dulce' signal ratio. adj.P.Val - p-value after multiple-tests correction by Ben- jamini and Hochberg method Additional file 2 Qualitative estimation of the intra-variation within Cucumis melo L.: PI414723 and 'Dulce' accessions. The document includes description of the experimental design and figure of comparison between two melon accessions, PI414723 and 'Dulce', intra- and inter-varia- tion. Abbreviations SFP: single-feature polymorphism; PPV: positive predictive value; MAS: marker- assisted selection; FDR: false discovery rate; BAC: bacterial artificial chromo- some; WGS: whole-genome scanning; gDNA: genomic DNA. Authors' contributions AS and RO conceived the idea of exploring melon variation using custom- designed microarrays. RO designed the array and performed all of the statisti- cal analyses. NK helped in integrating the experimental design for melon biol- ogy. VP, RB, YB and GT created the biological resources and did some of the wet work for validation of the results. SU was involved in the bioinformatics analysis of the array data and validation of the results. AS and RE contributed to the experimental design and testing of the microarray output. All authors read and approved the final manuscript. Acknowledgements This research was funded by a grant from the Agricultural Research Organiza- tion manager fund. Special thanks to Dr. Shirely Saban from the DNA Microar- ray Unit of the Weizmann Institute for helping with technical issues and performing the microarray hybridizations. The authors would also like to thank Dr. Zohar Yakhini and Prof. Yoav Benjamini for fruitful discussions. This is a con- tribution No. 113/2010 series from the Agriculture Research Organization, the Volcani Center, Bet Dagan, 50250, Israel. 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