Assessing the biological significance of primary structure consensus patterns using sequence databanks. I. Heat-shock and glucocorticoid control elements in eukaryotic promoters

Abstract

We describe FORTRAN 77 software allowing for convenient searching of any segmented and ambiguous pattern in the currently available protein or nucleotide sequence databanks. For proteins, this software can be instrumental in defining conserved functional domains among non-homologous overall primary structures. For nucleic acids, it is used in detecting complex and/or low consensus structural or regulatory patterns. As first applications we have studied the distribution of short consensus sequences believed to characterize heat-shock and glucocorticoid regulated promoters. This analysis allowed an evaluation of the specificity, probable role and thus biological significance of various regions of these consensus. In addition, the expression of several known genes are predicted to be heat-shock or glucocorticoid sensitive.