Let L be the test-period of random string, and be a decomposition of string Str into substrings of length L, where (if, substring is not complete; if M= 0, substring is empty).
Note that every substring is a subsequence, but a subsequence need not be a substring since the characters comprising a subsequence need not be contiguous.
External biological sequences are transformed to internal suffix tree structures, using TRELLIS algorithm [ 51]; sequence search operations such as exact sequence search, best match, and longest substring are allowed.
For each output sequence, the starting position in the input sequence where the matching substring begins is also provided.
To increase the matching coverage, substring matching is also performed.
The complexity of the lookup depends on the length of the substring being looked up (we assume a fixed maximal match length) and is therefore constant.
Search for repeats was performed as follows: first, all exactly matching 20-mer anchor substrings were identified in the nucleotide sequence of a bacterial or archaeal genome.
During alignment, the hash-based index is first scanned to identify the exact matches, then nearly identical maximal substrings are detected, and finally, bounded dynamic programming is used to extend the partial alignments.
Hence, we have made the substring search as 'optional' below the search window and the substring matches are displayed only if chosen by the user.
The results of substring matching were not evaluated, as the number of matching candidates increased to 24.88 per term on average.
