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Nucleic Acids Research, 1995, Vol. 23, No. 21 4471-4479
© 1995

Articles

Alignment editing and identification of consensus secondary structures for nucleic acid sequences: interactive use of dot matrix representations

Jeffrey P. Davis, Nebojsa Janjic, David Pribnow1 and Dominic A. Zichi*

NeXstar Pharmaceuticals Inc., 2860 Wilderness Place, Boulder, CO 80301, USA 1Oregon Health SciencesUniversity 3181 SW Sam Jackson Park Road, Portland, OR 97201, USA

*To whom correspondence should be addressed

Received August 21, 1995. Accepted September 20, 1995.

We present a computer-aided approach for identifying and aligning consensus secondary structure within a set of functionally related oligonucleotide sequences aligned by sequence. The method relies on visualization of secondary structure using a generalization of the dot matrix representation appropriate for consensus sequence data sets. An interactive computer program implementing such a visualization of consensus structure has been developed. The program allows for alignment editing, data and display filtering and various modes of base pair representation, Including co-variation. The utility of this approach Is demonstrated with four sample data sets derived from in vitro selection experiments and one data set comprising tRNA sequences.


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