Quasi-Linear-Time Algorithm for Longest Common Circular Factor

We introduce the Longest Common Circular Factor (LCCF) problem in which, given strings $S$ and $T$ of length $n$, we are to compute the longest factor of $S$ whose cyclic shift occurs as a factor of $T$. It is a new similarity measure, an extension of the classic Longest Common Factor. We show how to solve the LCCF problem in $O(n \log^5 n)$ time.

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

[2]  Costas S. Iliopoulos,et al.  Indexing Circular Patterns , 2008, WALCOM.

[3]  Jakub Radoszewski,et al.  On Abelian Longest Common Factor with and without RLE , 2018, Fundam. Informaticae.

[4]  D. Warburton,et al.  De novo balanced chromosome rearrangements and extra marker chromosomes identified at prenatal diagnosis: clinical significance and distribution of breakpoints. , 1991, American journal of human genetics.

[5]  Costas S. Iliopoulos,et al.  A fast and lightweight filter-based algorithm for circular pattern matching , 2014, BCB.

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

[7]  Gad M. Landau,et al.  Dynamic text and static pattern matching , 2007, TALG.

[8]  Szymon Grabowski,et al.  Average-optimal string matching , 2009, J. Discrete Algorithms.

[9]  Wojciech Rytter,et al.  Extracting powers and periods in a word from its runs structure , 2014, Theor. Comput. Sci..

[10]  Szymon Grabowski,et al.  Fast and Simple Circular Pattern Matching , 2013, ICMMI.

[11]  H. Edelsbrunner A new approach to rectangle intersections part I , 1983 .

[12]  Arnold L. Rosenberg,et al.  Rapid identification of repeated patterns in strings, trees and arrays , 1972, STOC.

[13]  Ely Porat,et al.  Locally Consistent Parsing for Text Indexing in Small Space , 2018, SODA.

[14]  Tomasz Kociumaka Efficient data structures for internal queries in texts , 2019 .

[15]  Costas S. Iliopoulos,et al.  Searching and Indexing Circular Patterns , 2017, Algorithms for Next-Generation Sequencing Data.

[16]  H. Wilf,et al.  Uniqueness theorems for periodic functions , 1965 .

[17]  Jorma Tarhio,et al.  Bit-Parallel Approximate Matching of Circular Strings with k Mismatches , 2017, ACM J. Exp. Algorithmics.

[18]  Eugene W. Myers,et al.  Suffix arrays: a new method for on-line string searches , 1993, SODA '90.

[19]  Richard C. T. Lee,et al.  Bit-Parallel Algorithms for Exact Circular String Matching , 2014, Comput. J..

[20]  Donald A. Adjeroh,et al.  Circular Pattern Discovery , 2015, Comput. J..

[21]  Donald A. Adjeroh,et al.  All-Against-All Circular Pattern Matching , 2012, Comput. J..

[22]  Costas S. Iliopoulos,et al.  Average-Case Optimal Approximate Circular String Matching , 2014, LATA.

[23]  Wojciech Rytter,et al.  Internal Pattern Matching Queries in a Text and Applications , 2013, SODA.

[24]  Costas S. Iliopoulos,et al.  Fast circular dictionary-matching algorithm , 2015, Mathematical Structures in Computer Science.

[25]  J. Yokota,et al.  Unbalanced translocation, a major chromosome alteration causing loss of heterozygosity in human lung cancer , 2008, Oncogene.

[26]  S. Muthukrishnan,et al.  On the sorting-complexity of suffix tree construction , 2000, JACM.

[27]  Domenico Cantone,et al.  Sequence Searching Allowing for Non-Overlapping Adjacent Unbalanced Translocations , 2018, WABI.

[28]  Kazuya Tsuruta,et al.  The "Runs" Theorem , 2014, SIAM J. Comput..

[29]  Gonzalo Navarro,et al.  Average-optimal single and multiple approximate string matching , 2004, JEAL.

[30]  Tomasz Kociumaka,et al.  String synchronizing sets: sublinear-time BWT construction and optimal LCE data structure , 2019, STOC.

[31]  M. K. Rudd,et al.  Unbalanced translocations arise from diverse mutational mechanisms including chromothripsis , 2015, Genome research.

[32]  Yo-Sub Han,et al.  Alignment with non-overlapping inversions and translocations on two strings , 2015, Theor. Comput. Sci..

[33]  Costas S. Iliopoulos,et al.  Fast algorithms for approximate circular string matching , 2014, Algorithms for Molecular Biology.