These criteria, described in greater detail below, impose requirements regarding the overall length of each similarity as well as the number and pattern of matches and mismatches within the similarity. The process of searching a matrix for similarities is described below. To begin the search for similarities, a matrix is set up between two particular chromosomes. One sequence is plotted along one axis of the matrix, the second along the other axis. This matrix is then scanned for similarities.
Similarities show up as diagonal lines of matches between the two chromosomes in the matrix.
The matrix is scanned twice, once for direct similarities, and a second time for inverted similarities. Explanation of Criteria Similarities are recorded for display by GDSV and GSV only if they meet a list of requirements. These requirements specify aspects of a similarity such as minimum overall number of matches or maximum overall number of base changes, insertions, and deletions. They also specify additional features such as minimum number of consecutive matches between any two mismatches, etc. These requirements are outlined in Table 1.