Pattern matching with pair correlation distance

Benny Porat, Ely Porat, Asaf Zur

Research output: Contribution to journalArticlepeer-review


In pattern matching with pair correlation distance problem, the goal is to find all occurrences of a pattern P of length m, in a text T of length n, where the distance between them is less than a threshold k. For each text location i, the distance is defined as the number of different kinds of mismatched pairs (α,β), between P and T[i ...i+m]. We present an algorithm with running time of O (min{|∑P|2 n log m, n(m log m) 2/3}) for this problem. Another interesting problem is the one-side pair correlation distance where it is desired to find all occurrences of P where the number of mismatched characters in P is less than k. For this problem, we present an algorithm with running time of O (min{|∑P|2 n log m, n √m log m}). © 2009 Springer Berlin Heidelberg.
Original languageEnglish
Pages (from-to)249-256
Number of pages8
JournalLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5280 LNCS
StatePublished - 31 Dec 2008
Event15th International Symposium on String Processing and Information Retrieval, SPIRE 2008 - Melbourne. VIC, Australia
Duration: 10 Nov 200812 Nov 2008

Bibliographical note

Funding Information:
I Research supported in part by the Israel Science Foundation (ISF) and by the Binational Science Foundation (BSF). ∗ Correspondingaddress:DepartmentofComputerScience,Bar-IlanUniversity,office:room305,52900Ramat-Gan,Israel.Tel.:+97235318866;fax: +972 3 736 0498. E-mail addresses: (B. Porat), (E. Porat), (A. Zur).


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