SEARCHPATTOOL: a new method for mining the most specific frequent patterns for binding sites with application to prokaryotic DNA sequences

Table 1 All frequent patterns for family A

Pattern	Matches(No seq, 1st position)	support	total
AA	[1,7] [7,5]	2	2
AG	[1,1] [2,3] [2,5] [4,4] [6,4] [7,1]	4	6
AT	[3,6] [4,2] [5,5] [6,2]	2	4
A.A	[2,3] [3,6] [4,2] [6,2]	3	4
A.C	[1,1] [2,5] [7,1]	2	3
A..G	[2,3] [4,2] [4,4] [6,2] [7,1]	4	5
A...C	[1,1] [2,3] [4,4]	2	3
A....A	[3,3] [7,1]	2	2

For each pattern, the occurrences of the patterns in the input sequences (Matches) -within the bracket you find the number of sequence (No seq) and the first position of the pattern (1st position)-, the number of matching sequences (support) and the total number of occurrences (total) are shown. All these patterns have a support greater or equal to 2.

ISSN: 1471-2105