Abstract
In pattern matching with the 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 {| ΣP |2 n log m, n (m log m)frac(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 {| ΣP | n log m, n sqrt(m log m)}).
| Original language | English |
|---|---|
| Pages (from-to) | 587-590 |
| Number of pages | 4 |
| Journal | Theoretical Computer Science |
| Volume | 407 |
| Issue number | 1-3 |
| DOIs | |
| State | Published - 6 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: [email protected] (B. Porat), [email protected] (E. Porat), [email protected] (A. Zur).
Funding
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: [email protected] (B. Porat), [email protected] (E. Porat), [email protected] (A. Zur).
| Funders | Funder number |
|---|---|
| United States-Israel Binational Science Foundation | |
| Israel Science Foundation |