title: Derivation of a scale-independent parameter which characterizes genetic sequence comparisons.
abstract: A new method of quantifying the similarity between genetic sequences is presented. The method makes use of the finding that sequence comparisons expressed in binary vector form have an associated scale-independent parameter, D. This parameter is represented in the function M(S,n) = (N) (en/enD), where S is the vector, n represents the window size which is allowed to vary, N is a constant, and D is the scale-independent measure of homology. By comparing two sequences using this method, a unimodal, symmetric distribution of D values associated with the frameshifted vectors is obtained. The degree of sequence similarity is determined by the distribution of these parameters. A set of sequences of evolutionary interest coding for glyceraldehyde-3-phosphate dehydrogenases and mammalian insulins is compared using this methodology. The results confirm evolutionary tree distances calculated using different procedures. Since a z score can be calculated for each comparison, the method allows for the rapid identification of sequence homologies ranked according to the probability of occurrence. This unique scale-independent measure of similarity allows contrasts and comparisons between any two sequence fragments using all available order information.
authors.affiliation: Brown University School of Medicine, Roger Williams Hospital, Providence, Rhode Island 02908.
authors.forename: P B
authors.initials: PB
authors.lastname: DePetrillo
authors.forename: A J
authors.initials: AJ
authors.lastname: Butte
mesh_terms: D000199:Actins / Q000235:genetics; D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D004247:DNA / Q000235:genetics*; D005069:Evaluation Studies as Topic; D005987:Glyceraldehyde-3-Phosphate Dehydrogenases / Q000235:genetics; D006801:Humans; D007328:Insulin / Q000235:genetics; D008969:Molecular Sequence Data; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D000199:Actins; D007328:Insulin; D004247:DNA; D005987:Glyceraldehyde-3-Phosphate Dehydrogenases