Discover 1: a new program to search for unusually represented DNA motifs

DISCOVER1 (DIStribution COunter VERsion 1) is a new program that can identify DNA motifs occurring with a high deviation from the expected frequency. The program generates families of patterns, each family having a common set of defined bases. Undefined bases are inserted amongst the defined bases in different ways, thus generating the diverse patterns of each family. The occurrences of the different patterns are then compared and analysed within each family, assuming that all patterns should have the same probability of occurrence. An extensive use of computer memory, combined with the immediate sorting of counts by address calculation allow a complete counting of all DNA motifs on a single pass on the DNA sequence. This approach offers a very fast way to search for unusually distributed patterns and can identify inexact patterns as well as exact patterns.