Pattern matching and consensus problems on weighted sequences and profiles

Tomasz Kociumaka, Solon P. Pissis, Jakub Radoszewski

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

Abstract

We study pattern matching problems on two major representations of uncertain sequences used in molecular biology: weighted sequences (also known as position weight matrices, PWM) and profiles (i.e., scoring matrices). In the simple version, in which only the pattern or only the text is uncertain, we obtain efficient algorithms with theoretically-provable running times using a variation of the lookahead scoring technique. We also consider a general variant of the pattern matching problems in which both the pattern and the text are uncertain. Central to our solution is a special case where the sequences have equal length, called the consensus problem. We propose algorithms for the consensus problem parameterized by the number of strings that match one of the sequences. As our basic approach, a careful adaptation of the classic meet-in-the-middle algorithm for the knapsack problem is used. On the lower bound side, we prove that our dependence on the parameter is optimal up to lower-order terms conditioned on the optimality of the original algorithm for the knapsack problem.

Original languageEnglish
Title of host publication27th International Symposium on Algorithms and Computation, ISAAC 2016
EditorsSeok-Hee Hong
PublisherSchloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
Pages46.1-46.12
ISBN (Electronic)9783959770262
DOIs
Publication statusPublished - 1 Dec 2016
Externally publishedYes
Event27th International Symposium on Algorithms and Computation, ISAAC 2016 - Sydney, Australia
Duration: 12 Dec 201614 Dec 2016

Publication series

NameLeibniz International Proceedings in Informatics, LIPIcs
Volume64
ISSN (Print)1868-8969

Conference

Conference27th International Symposium on Algorithms and Computation, ISAAC 2016
CountryAustralia
CitySydney
Period12/12/1614/12/16

Keywords

  • Position weight matrix
  • Profile matching
  • Weighted sequence

Fingerprint

Dive into the research topics of 'Pattern matching and consensus problems on weighted sequences and profiles'. Together they form a unique fingerprint.

Cite this