We present an efficient algorithm for finding all approximate occurrences of a given pattern $p$ of length $m$ in a text $t$ of length $n$ allowing for translocations of equal length adjacent factors and inversions of factors. The algorithm is based on an efficient filtering method and has an $\bigO(nm\max(\alpha, \beta))$-time complexity in the worst case and $\bigO(\max(\alpha, \beta))$-space complexity, where $\alpha$ and $\beta$ are respectively the maximum length of the factors involved in any translocation and inversion. Moreover we show that under the assumptions of equiprobability and independence of characters our algorithm has a $\bigO(n)$ average time complexity, whenever $\sigma = \Omega(\log m / \log\log^{1-\epsilon} m)$, where $\epsilon > 0$ and $\sigma$ is the dimension of the alphabet. Experiments show that the new proposed algorithm achieves very good results in practical cases
String Matching with Inversions and Translocations in Linear Average Time (Most of the Time)
FARO, SIMONE;
2011-01-01
Abstract
We present an efficient algorithm for finding all approximate occurrences of a given pattern $p$ of length $m$ in a text $t$ of length $n$ allowing for translocations of equal length adjacent factors and inversions of factors. The algorithm is based on an efficient filtering method and has an $\bigO(nm\max(\alpha, \beta))$-time complexity in the worst case and $\bigO(\max(\alpha, \beta))$-space complexity, where $\alpha$ and $\beta$ are respectively the maximum length of the factors involved in any translocation and inversion. Moreover we show that under the assumptions of equiprobability and independence of characters our algorithm has a $\bigO(n)$ average time complexity, whenever $\sigma = \Omega(\log m / \log\log^{1-\epsilon} m)$, where $\epsilon > 0$ and $\sigma$ is the dimension of the alphabet. Experiments show that the new proposed algorithm achieves very good results in practical casesFile | Dimensione | Formato | |
---|---|---|---|
2011 GrabowskyFaroGiaquinta IPL.pdf
solo gestori archivio
Tipologia:
Versione Editoriale (PDF)
Licenza:
Non specificato
Dimensione
158.17 kB
Formato
Adobe PDF
|
158.17 kB | Adobe PDF | Visualizza/Apri |
I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.