title: DNAMAT: an efficient graphic matrix sequence homology algorithm and its application to structural analysis.
abstract: We present a fast algorithm to produce a graphic matrix representation of sequence homology. The algorithm is based on lexicographical ordering of fragments. It preserves most of the options of a simple naive algorithm with a significant increase in speed. This algorithm was the bais for a program, called DNAMAT, that has been extensively tested during the last three years at the Weizmann Institute of Science and has proven to be very useful. In addition we suggest a way to extend our approach to analyse a series of related DNA or RNA sequences, in order to determine certain common structural features. The analysis is done by 'summing' a set of dot-matrices to produce an overall matrix that displays structural elements common to most of the sequences. We give an example of this procedure by analysing tRNA sequences.
authors.affiliation: Department of Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: R
authors.initials: R
authors.lastname: Unger
authors.forename: D
authors.initials: D
authors.lastname: Harel
authors.forename: J L
authors.initials: JL
authors.lastname: Sussman
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D012343:RNA, Transfer; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D012343:RNA, Transfer