The melanoma and melanocyte cell lines have irreversible gene variations that constantly change DNA sequences, chromosomal alterations and gene mutations. DNA binding proteins such as transcription factors or modified histone proteins and gene mutations within melanoma and melanocyte cell lines are identified using genome-wide Chip-Seq method. Different Chip-Seq algorithms are used to read the whole genome sequencing data to align reads and find the differential gene expressions, gene-protein expression patterns, gene alterations and gene interaction that helps to provide novel prognostic and potential therapeutic targets. Here, HEMn_H3K4me3 of reference genome build hg18 were mapped with Illumina genome analyzer. The aligned reads of gap size was set at FDR ≤5% was estimated with E-value divided by number of identified candidate domains. DNA methylation and histone modifications of genes such as HOXD29, COLA2, HSPB6 and MT1G were validated by potential epigenetic targets and are used as potential drug targets
