On the shared substring alignment problem

Gad M. Landau; Michal Ziv-Ukelson

On the shared substring alignment problem

Gad M. Landau, Michal Ziv-Ukelson

Research output: Contribution to conference › Paper › peer-review

Abstract

A new problem in sequence comparison, given a set of strings S₁, S₂ ... S_c and a target string T S_i = B_iY F_i is introduced. Y is the subsequence common to all of strings S_i. The goal is to compute similarity of all strings S_i with T, without computing the part of Y again and again. How to reduce the O(nl) runtime work for the common subsequence Y in each string to O(n), at the cost of only O(n²+nl) work at preprocessing time, where n is target size and l is the size of Y.

Original language	English
Pages	804-814
Number of pages	11
State	Published - 2000
Externally published	Yes
Event	11th Annual ACM-SIAM Symposium on Discrete Algorithms - San Francisco, CA, USA Duration: 9 Jan 2000 → 11 Jan 2000

Conference

Conference	11th Annual ACM-SIAM Symposium on Discrete Algorithms
City	San Francisco, CA, USA
Period	9/01/00 → 11/01/00

ASJC Scopus subject areas

Software
General Mathematics

Cite this

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title = "On the shared substring alignment problem",

abstract = "A new problem in sequence comparison, given a set of strings S1, S2 ... Sc and a target string T Si = BiY Fi is introduced. Y is the subsequence common to all of strings Si. The goal is to compute similarity of all strings Si with T, without computing the part of Y again and again. How to reduce the O(nl) runtime work for the common subsequence Y in each string to O(n), at the cost of only O(n2+nl) work at preprocessing time, where n is target size and l is the size of Y.",

author = "Landau, {Gad M.} and Michal Ziv-Ukelson",

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AB - A new problem in sequence comparison, given a set of strings S1, S2 ... Sc and a target string T Si = BiY Fi is introduced. Y is the subsequence common to all of strings Si. The goal is to compute similarity of all strings Si with T, without computing the part of Y again and again. How to reduce the O(nl) runtime work for the common subsequence Y in each string to O(n), at the cost of only O(n2+nl) work at preprocessing time, where n is target size and l is the size of Y.

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M3 - Paper

AN - SCOPUS:0033902899

SP - 804

EP - 814

T2 - 11th Annual ACM-SIAM Symposium on Discrete Algorithms

Y2 - 9 January 2000 through 11 January 2000

ER -

On the shared substring alignment problem

Abstract

Conference

ASJC Scopus subject areas

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