title: A readable and space-efficient DNA sequence representation: application to caulimoviral DNAs.
abstract: 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.
authors.affiliation: Department of Biochemistry, Oklahoma State University, Stillwater 74078-0454.
authors.forename: U
authors.initials: U
authors.lastname: Melcher
mesh_terms: D001483:Base Sequence; D003196:Computer Graphics; D004247:DNA / Q000235:genetics*; D004279:DNA, Viral / Q000235:genetics; D008969:Molecular Sequence Data; D009029:Mosaic Viruses / Q000235:genetics; D009690:Nucleic Acid Conformation; D012689:Sequence Homology, Nucleic Acid; D013539:Simian virus 40 / Q000235:genetics; D012984:Software
chemical_list: D004279:DNA, Viral; D004247:DNA