SGER: Identifying Regulatory Motifs in Genomes

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Sequence motifs in genomes are one of the ways genes are regulated in a coordinate fashion. The simple occurrence and correlation of sequences with specific function is supportive of the hypothesis that a given distribution is involved in regulation. The ability to identify motifs both by sequence and location, as well as to indicate a likelihood score will enable the generation of a series of possible regulatory motifs in both Arabidopsis and E. elegans. Introns as well as upstream regions will be examined. Genes with similar sequences will be clustered and the analysis compared with microarray data to determine possible biological significance. A similar approach could be extended from DNA sequence to short amino acid motifs to help cluster the proteome of each organism.