On Computing Average Common Substring Over Run Length Encoded Sequences

Keywords

Compression; RL Encoding; String Algorithms; Suffix Trees

Abstract

The Average Common Substring (ACS) is a popular alignment-free distance measure for phylogeny reconstruction. The ACS of a sequence X[1, x] w.r.t. another sequence Y[1, y] is ACS(X, Y) = 1 x Σ i=1 x max j lcp(X[i, x], Y[j, y]) The lcp(·, ·) of two input sequences is the length of their longest common prefix. The ACS can be computed in O(n) space and time, where n = x + y is the input size. The compressed string matching is the study of string matching problems with the following twist: the input data is in a compressed format and the underling task must be performed with little or no decompression. In this paper, we revisit the ACS problem under this paradigm where the input sequences are given in their run-length encoded format. We present an algorithm to compute ACS(X, Y) in O(N logN) time using O(N) space, where N is the total length of sequences after run-length encoding.

Publication Date

1-1-2018

Publication Title

Fundamenta Informaticae

Volume

163

Issue

3

Number of Pages

267-273

Document Type

Article; Proceedings Paper

Personal Identifier

scopus

DOI Link

https://doi.org/10.3233/FI-2018-1743

Socpus ID

85056345884 (Scopus)

Source API URL

https://api.elsevier.com/content/abstract/scopus_id/85056345884

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