Surveys for conserved noncoding sequences (CNS) among genes from monocot cereal 
species were conducted to assess the general properties of CNS in grass genomes 
and their correlation with known promoter regulatory elements. Initial 
comparisons of 11 orthologous maize-rice gene pairs found that previously 
defined regulatory motifs could be identified within short CNS but could not be 
distinguished reliably from random sequence matches. Among the different 
phylogenetic footprinting algorithms tested, the VISTA tool yielded the most 
informative alignments of noncoding sequence. VISTA was used to survey for CNS 
among all publicly available genomic sequences from maize, rice, wheat, barley, 
and sorghum, representing >300 gene comparisons. Comparisons of orthologous 
maize-rice and maize-sorghum gene pairs identified 20 bp as a minimal length 
criterion for a significant CNS among grass genes, with few such CNS found to be 
conserved across rice, maize, sorghum, and barley. The frequency and length of 
cereal CNS as well as nucleotide substitution rates within CNS were consistent 
with the known phylogenetic distances among the species compared. The 
implications of these findings for the evolution of cereal gene promoter 
sequences and the utility of using the nearly completed rice genome sequence to 
predict candidate regulatory elements in other cereal genes by phylogenetic 
footprinting are discussed.