A high speed, high capacity homology matrix: zooming through SV40 and polyoma

Nucleic Acids Res. 1982 Aug 11;10(15):4765-82. doi: 10.1093/nar/10.15.4765.


We present a new homology matrix program which owes its basic conception to the two-dimensional dot matrices previously described (1,2), but has important improvements and new features. It scores sequence homology over an adjustable range and plots the scores which are above an operator-determined filtration level. Its powerful noise-filtration system, capacity for compression without much loss of information, and speed of execution make this program a valuable tool in the analysis of homologies, internal direct repeats and reverse repeats, including palindromic sequences. The properties of the program are exemplified by analysis of SV40 and polyoma DNA sequences.

Publication types

  • Comparative Study
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Composition
  • Base Sequence
  • DNA, Viral / genetics*
  • Nucleic Acid Conformation
  • Polyomavirus / genetics*
  • Repetitive Sequences, Nucleic Acid
  • Simian virus 40 / genetics*
  • Species Specificity


  • DNA, Viral