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 -