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© 1988 IRL Press Ltd

A readable and space-efficient DNA sequence representation: application to caulimoviral DNAs

Ulrich Melcher

Department of Biochemistry, Oklahoma State University Stillwater, OK 74078-0454, USA

A new representation of nucleotide sequence information has been devised to allow the clear presentation of large amounts of sequence information in a limited amount of space. Nucleotide sequences of DNA are represented by squares in three vertically aligned positions for each nucleotide. The squares represent, from top to bottom: a purine, a guanine or cytosine and a pyrimidine. The representation provides a simultaneous representation of both strands of double-stranded DNA and can be easily scanned visually for a variety of sequence features. Biologically important features of the DNA sequence near the origin of SV40 replication are easily recognized. The representation was also used to identify possibly base-paired stems in caulimoviral transcripts that may be of significance for viral replication.

Received on June 22, 1987; accepted on October 22, 1987

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