Methodology for alignment and identification of CNEs between Fugu and mammalian orthologous genomic sequences. Boundaries of CNE-containing regions are identified through a CNE synteny map created using a stringent whole genome comparison of the non-coding portions of the human and Fugu genomes . The genomic regions to be aligned are then expanded past the map boundaries up to the next nearest known genes. Trans-dev genes in the region are determined using appropriate GO ontologies and/or InterPro domains. Orthologous sequence corresponding to this expanded region in human is then extracted from mouse, rat and/or dog genomes. Sequences are masked for repeats and are aligned using MLAGAN (identifying sequences conserved in the same order along the sequence) and SLAGAN (to identify conserved elements that have undergone rearrangement in one or more lineages). CNEs are identified using VISTA and filtered to exclude any that overlap known coding exons or ncRNAs. As an added stringency filter, only those CNEs that are conserved in at last four divergent vertebrate genomes (including Fugu) are retained to avoid spurious matches.