TY - CHAP

T1 - Sparse normalized local alignment

AU - Efraty, Nadav

AU - Landau, Gad M.

PY - 2004

Y1 - 2004

N2 - Given two strings, X and Y, both of length O(n) over alphabet ∑, a basic problem (local alignment) is to find pairs of similar substrings, one from X and one from Y. For substrings X' and Y' from X and Y, respectively, the metric we use to measure their similarity is normalized alignment value: LCS(X', Y')/(|X'| + |Y'|). Given an integer M we consider only those substrings whose LCS length is at least M. We present an algorithm that reports the pairs of substrings with the highest normalized alignment value in O(n log |∑| + r M log log n) time (r - the number of matches between X and Y). We also present an O(n log |∑| + r L log log n) algorithm (L = LCS(X, Y)) that reports all substring pairs with a normalized alignment value above a given threshold.

AB - Given two strings, X and Y, both of length O(n) over alphabet ∑, a basic problem (local alignment) is to find pairs of similar substrings, one from X and one from Y. For substrings X' and Y' from X and Y, respectively, the metric we use to measure their similarity is normalized alignment value: LCS(X', Y')/(|X'| + |Y'|). Given an integer M we consider only those substrings whose LCS length is at least M. We present an algorithm that reports the pairs of substrings with the highest normalized alignment value in O(n log |∑| + r M log log n) time (r - the number of matches between X and Y). We also present an O(n log |∑| + r L log log n) algorithm (L = LCS(X, Y)) that reports all substring pairs with a normalized alignment value above a given threshold.

UR - http://www.scopus.com/inward/record.url?scp=35048901947&partnerID=8YFLogxK

U2 - 10.1007/978-3-540-27801-6_25

DO - 10.1007/978-3-540-27801-6_25

M3 - Chapter

AN - SCOPUS:35048901947

SN - 354022341X

SN - 9783540223412

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 333

EP - 346

BT - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

A2 - Sahinalp, Suleyman Cenk

A2 - Muthukrishnan, S.

A2 - Dogrusoz, Ugur

PB - Springer Verlag

ER -