Consequences of faster alignment of sequences

Amir Abboud, Virginia Vassilevska Williams, Oren Weimann

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review


The Local Alignment problem is a classical problem with applications in biology. Given two input strings and a scoring function on pairs of letters, one is asked to find the substrings of the two input strings that are most similar under the scoring function. The best algorithms for Local Alignment run in time that is roughly quadratic in the string length. It is a big open problem whether substantially subquadratic algorithms exist. In this paper we show that for all ε > 0, an O(n2-ε) time algorithm for Local Alignment on strings of length n would imply breakthroughs on three longstanding open problems: it would imply that for some δ > 0, 3SUM on n numbers is in O(n2-δ) time, CNF-SAT on n variables is in O((2-δ) n) time, and Max Weight 4-Clique is in O(n4-δ) time. Our result for CNF-SAT also applies to the easier problem of finding the longest common substring of binary strings with don't cares. We also give strong conditional lower bounds for the more general Multiple Local Alignment problem on k strings, under both k-wise and SP scoring, and for other string similarity problems such as Global Alignment with gap penalties and normalized Longest Common Subsequence.

Original languageEnglish
Title of host publicationAutomata, Languages, and Programming - 41st International Colloquium, ICALP 2014, Proceedings
PublisherSpringer Verlag
Number of pages13
EditionPART 1
ISBN (Print)9783662439470
StatePublished - 2014
Event41st International Colloquium on Automata, Languages, and Programming, ICALP 2014 - Copenhagen, Denmark
Duration: 8 Jul 201411 Jul 2014

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
NumberPART 1
Volume8572 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference41st International Colloquium on Automata, Languages, and Programming, ICALP 2014

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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