Patent ID: 7720614

Claim:
A method of identifying a cis-regulatory module, comprising: a) determining, using a suitably programmed computer, sequence similarities significantly greater than random expectation on selected genome sequences from two or more species in sequences that lie outside of protein coding regions, wherein the evolutionary distance between the two or more species is selected from the group consisting of about 1 to 18 million years; b) sorting the similarities for conserved patches of single nucleotide polymorphisms (SNPs) and insertion/deletions (indels); c) constructing a computational map of SNPs/indels, which SNPs/indels have occurrence rates within the patches that are suppressed when compared to sequences which flank the patches, wherein a suppressed occurrence rate within the patches for SNPs exhibits a decrease in frequency of about 30% to 50% when compared to flanking sequences, and wherein the flanking sequences comprise large indels having a length of at least 6-10 nucleotides; d) computing a moving window SNPs/indels-intensity parameter based on the patches; and e) moving the window across a query sequence; f) selecting patches in the query sequence which significantly match the window SNPs/indels-intensity parameter; and g) operably linking a sequence comprising a patch selected in step (f) to a reporter sequence in a vector, wherein a cis-regulatory module is identified in a patch in the query sequence if the reporter sequence is expressed in a host comprising the vector, thereby identifying a cis-regulatory module.