Normalized similarity of RNA sequences

Rolf Backofen, Danny Hermelin, Gad M. Landau, Oren Weimann

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

Abstract

We introduce a normalized version of the LCS metric as a new local similarity measure for comparing two RNAs. An O(n2m lg m) time algorithm is presented for computing the maximum normalized score of two RNA sequences, where n and m are the lengths of the sequences and n ≤ m. This algorithm has the same time complexity as the currently best known global LCS algorithm.

Original languageEnglish
Title of host publicationString Processing and Information Retrieval - 12th International Conference, SPIRE 2005, Proceedings
Pages360-369
Number of pages10
DOIs
StatePublished - 2005
Event12th International Conference on String Processing and Information Retrieval, SPIRE 2005 - Buenos Aires, Argentina
Duration: 2 Nov 20054 Nov 2005

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3772 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference12th International Conference on String Processing and Information Retrieval, SPIRE 2005
Country/TerritoryArgentina
CityBuenos Aires
Period2/11/054/11/05

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science (all)

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