Faster Recovery of Approximate Periods over Edit Distance

The approximate period recovery problem asks to compute all approximate word-periods of a given word S of length n: all primitive words P (\(|P|=p\)) which have a periodic extension at edit distance smaller than \(\tau _p\) from S, where \(\tau _p = \lfloor \frac{n}{(3.75+\epsilon )\cdot p} \rfloor \) for some \(\epsilon >0\). Here, the set of periodic extensions of P consists of all finite prefixes of \(P^\infty \).

[1]  Vincent A. Fischetti,et al.  Identifying Periodic Occurrences of a Template with Applications to Protein Structure , 1993, Inf. Process. Lett..

[2]  Gary Benson,et al.  Tandem repeats over the edit distance , 2007, Bioinform..

[3]  V. Y. Popov The approximate period problem for DNA alphabet , 2003, Theor. Comput. Sci..

[4]  Gad M. Landau,et al.  Fast Parallel and Serial Approximate String Matching , 1989, J. Algorithms.

[5]  Wojciech Rytter,et al.  Jewels of stringology : text algorithms , 2002 .

[6]  Gregory Kucherov,et al.  Finding Approximate Repetitions under Hamming Distance , 2001, ESA.

[7]  Dina Sokol,et al.  Speeding up the detection of tandem repeats over the edit distance , 2014, Theor. Comput. Sci..

[8]  Jeong Seop Sim,et al.  Approximate periods of strings , 2001, Theor. Comput. Sci..

[9]  Andrzej Ehrenfeucht,et al.  Efficient Detection of Quasiperiodicities in Strings , 1993, Theor. Comput. Sci..

[10]  Ely Porat,et al.  Cycle Detection and Correction , 2010, ICALP.

[11]  Dan Gusfield Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology , 1997 .

[12]  Gad M. Landau,et al.  Period recovery of strings over the Hamming and edit distances , 2017, Theor. Comput. Sci..

[13]  Gad M. Landau,et al.  Locating maximal approximate runs in a string , 2017, Theor. Comput. Sci..

[14]  Costas S. Iliopoulos,et al.  Optimal Superprimitivity Testing for Strings , 1991, Inf. Process. Lett..

[15]  Wojciech Rytter,et al.  Jewels of stringology , 2002 .

[16]  Maxime Crochemore,et al.  Algorithms on strings , 2007 .

[17]  Wojciech Rytter,et al.  A Linear-Time Algorithm for Seeds Computation , 2011, SODA.

[18]  Dany Breslauer,et al.  An On-Line String Superprimitivity Test , 1992, Inf. Process. Lett..

[19]  Yin Li,et al.  Computing the Cover Array in Linear Time , 2001, Algorithmica.