Cancer Institute A national cancer institute
designated cancer center

Atul Butte

Publication Details

  • DERIVATION OF A SCALE-INDEPENDENT PARAMETER WHICH CHARACTERIZES GENETIC SEQUENCE COMPARISONS COMPUTERS AND BIOMEDICAL RESEARCH DePetrillo, P. B., Butte, A. J. 1993; 26 (6): 517-540

    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.

    View details for Web of Science ID A1993MM97500003

    View details for PubMedID 8112054

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