On computing average common substring over run length encoded sequences
From MaRDI portal
Abstract: The Average Common Substring (ACS) is a popular alignment-free distance measure for phylogeny reconstruction. 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(Nlog N) time using O(N) space, where N is the total length of sequences after run-length encoding.
Recommendations
- A fast and simple algorithm for computing the longest common subsequence of run-length encoded strings
- Longest common subsequence between run-length-encoded strings: a new algorithm with improved parallelism
- Fast algorithms for computing the constrained LCS of run-length encoded strings
- Matching for run-length encoded strings
- Efficient Alignment Free Sequence Comparison with Bounded Mismatches
Cited in
(2)
This page was built for publication: On computing average common substring over run length encoded sequences
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q4611215)
