An interactive dot matrix system for locating potentially significant features in nucleic acid molecules.
An interactive computer system using a dot matrix approach has been developed and used to determine potentially significant features due to distortions in the B-DNA helix as a result of variations of purine and pyrimidine patterns. Sequences were compared using matrices which were generated using the Calladine-Dickerson rules (C.R. Calladine, J. Mol. Biol. 161, 343-352, 1982 and R.E. Dickerson, J. Mol. Biol. 166, 419-441, 1983). Having control over various parameters to enhance different aspects of the visual appearance of these matrices was helpful in discovering patterns that were not known a priori. Specifically, it was found that a pattern of alternating doublets of purines and pyrimidines appear to exist in regulatory regions. This event is shown to be beyond probabilistic expectation.
Shapiro
B A
BA
Laboratory of Mathematical Biology, National Cancer Institute, Frederick Cancer Research Facility, Maryland 21701.
Nussinov
R
R
Lipkin
L E
LE
Maizel
J V
JV
D001483:Base Sequence; D004247:DNA / Q000648:ultrastructure; D003626:Data Display; D005814:Genes, Viral; D007091:Image Processing, Computer-Assisted; D008328:Man-Machine Systems; D009690:Nucleic Acid Conformation; D011120:Polyomavirus / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid; D012190:Retroviridae / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D013539:Simian virus 40 / Q000235:genetics; D012984:Software
D004247:DNA