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

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.