We aimed to devise an appropriate method to directly link the fluorescence profile of chromosomal copy number alterations detected by chromosomal comparative genomic hybridization (cCGH) or any other hybridization or staining information with the genome sequence data. Our goal was to establish an internal anchoring system that could facilitate profile alignment and thus increase the resolution of cCGH. We were able to achieve the alignment of chromosomes with gene mapping data by superimposition of (a) the fluorescence intensity pattern of a sequence-specific fluorochrome (GGCC binding specificity), (b) the cCGH fluorescence intensity profile of individual chromosomes, and (c) the GGCC motif density profile extracted from a genome sequence database. The adjustment of these three pieces of information allowed us to precisely localize, in cytobands and mega base pairs (Mb), regions of genomic alterations such as gene amplifications, gains, or losses. The combined visualization of sequence information and cCGH data together with application of the Warp tool, presented here, considerably improves the cCGH accuracy by increasing its resolution from 10 to 20 Mb to less than 2 Mb.