Locating alignments with k differences for nucleotide and amino acid sequences.
Given two sequences, a pattern of length m, a text of length n and a positive integer k, we give two algorithms. The first finds all occurrences of the pattern in the text as long as these do not differ from each other by more than k differences. It runs in O(nk) time. The second algorithm finds all subsequence alignments between the pattern and the test with at most k differences. This algorithm runs in O(nmk) time, is very simple and easy to program.
Landau
G M
GM
Department of Computer Science, School of Mathematical Sciences, Tel Aviv University, Israel.
Vishkin
U
U
Nussinov
R
R
D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D007256:Information Systems; D012984:Software