ALIGNMENT EDITING AND IDENTIFICATION OF CONSENSUS SECONDARY STRUCTURES FOR NUCLEIC-ACID SEQUENCES - INTERACTIVE USE OF DOT MATRIX REPRESENTATIONS

We present a computer-aided approach for identifying and aligning cons ensus secondary structure within a set of functionally related oligonu cleotide sequences aligned by sequence, The method relies on visualiza tion of secondary structure using a generalization of the dot matrix r epresentation appropriate for consensus sequence data sets, An interac tive computer program implementing such a visualization of consensus s tructure has been developed, The program allows for alignment editing, data and display filtering and various modes of base pair representat ion, including co-variation, The utility of this approach is demonstra ted with four sample data sets derived from in vitro selection experim ents and one data set comprising tRNA sequences.