EARS detects alignment-conserved regions in promoter sequences. It is used to compare orthologous plant promoters to find sequences conserved across all orthologs. First, a template sequence to which all others will be compared must be chosen along with a window size (60bp is sufficient to yield result in most cases). Up to 10 orthologs may be used in comparisons. Each sequence should be given a unique name for simple interpretation of the results.
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Plant J. 2010 Oct;64(1):165-76. doi: 10.1111/j.1365-313X.2010.04314.x. Epub 2010 Sep 16.
Evolutionary analysis of regulatory sequences (EARS) in plants.
Picot E1, Krusche P, Tiskin A, Carré I, Ott S.