Back to results
US 2006/0141513 A1Published application
Method for recognition and recovery of cis-regulatory modules
AssigneeCalifornia Institute of Technology
InventorsEric Davidson, Robert Cameron
Life of this patent
Estimating the term…
Abstract
A computational method is described which uses the process of cis-regulatory module evolution to identify conserved sequence patches which exhibit suppression of change by snp/indel occurrence, in the absence of having to execute multiple interspecific sequence comparison analysis, including libraries, and arrays that contain such cis-regulatory modules.
Claims21
A method of identifying a cis-regulatory module, comprising:
- a) determining sequence similarities significantly greater than random expectation on selected genome sequences from two or more closely related species in sequences that lie outside of protein coding regions;
- b) sorting the similarities for conserved patches of single nucleotide polymorphisms (SNPs) and insertion/deletions (indels);
- c) constructing a computational map of SNPs/indels, wherein the SNPs/indels have occurrence rates within the patches which are suppressed when compared to flanking sequences;
- d) computing a moving window snp/indel intensity parameter based on the patches;
- and
- e) moving the window across a query sequence,
- wherein a putative cis-regulatory module is identified if a region in the query sequence significantly matches the window parameter.
4 more elements
Dependencies are inferred from the claim text.