Locating well-conserved regions within a pairwise alignment

Within a single alignment of two DNA sequences or two protein sequences, some regions may be much better conserved than others. Such strong conservation may reveal a region that possesses an important function. When alignments are so long that it is infeasible, or at least undesirable, to inspect them in complete detail, it is helpful to have an automatic process that computes information about the varying degree of conservation along the alignment and displays the information in a graphical representation that is readily assimilated. This paper presents methods for computing several such 'robustness measures' at each position of a given alignment. These methods are all very space-efficient; they use only space proportional to the sum of the two sequence lengths. To illustrate their effectiveness, one of the methods is used to locate particularly well-conserved regions in the beta-globin gene locus control region and in the 5' flank of the gamma-globin gene.