TY - GEN
T1 - Two Algorithms for LCS Consecutive Suffix Alignment
AU - Landau, Gad M.
AU - Myers, Eugene
AU - Ziv-Ukelson, Michal
PY - 2004/1/1
Y1 - 2004/1/1
N2 - The problem of aligning two sequences A and B to determine their similarity is one of the fundamental problems in pattern matching. A challenging, basic variation of the sequence similarity problem is the incremental string comparison problem, denoted Consecutive Suffix Alignment, which is, given two strings A and B, to compute the alignment solution of each suffix of A versus B. Here, we present two solutions to the Consecutive Suffix Alignment Problem under the LCS metric. The first solution is an O(nL) time and space algorithm for constant alphabets, where n is the size of the compared strings and L < n denotes the size of the LCS of A and B. The second solution is an O(nL + n log |∑|) time and O(L) space algorithm for general alphabets, where S denotes the alphabet of the compared strings. (Note that \∑\ < n.)
AB - The problem of aligning two sequences A and B to determine their similarity is one of the fundamental problems in pattern matching. A challenging, basic variation of the sequence similarity problem is the incremental string comparison problem, denoted Consecutive Suffix Alignment, which is, given two strings A and B, to compute the alignment solution of each suffix of A versus B. Here, we present two solutions to the Consecutive Suffix Alignment Problem under the LCS metric. The first solution is an O(nL) time and space algorithm for constant alphabets, where n is the size of the compared strings and L < n denotes the size of the LCS of A and B. The second solution is an O(nL + n log |∑|) time and O(L) space algorithm for general alphabets, where S denotes the alphabet of the compared strings. (Note that \∑\ < n.)
UR - http://www.scopus.com/inward/record.url?scp=35048833282&partnerID=8YFLogxK
U2 - 10.1007/978-3-540-27801-6_13
DO - 10.1007/978-3-540-27801-6_13
M3 - Conference contribution
AN - SCOPUS:35048833282
SN - 354022341X
SN - 9783540223412
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 173
EP - 193
BT - Combinatorial Pattern Matching
A2 - Sahinalp, Suleyman Cenk
A2 - Muthukrishnan, S.
A2 - Dogrusoz, Ugur
PB - Springer Verlag
T2 - 15th Annual Symposium on Combinatorial Pattern Matching
Y2 - 5 July 2004 through 7 July 2004
ER -