An Average-Case Efficient Two-Stage Algorithm for Enumerating All Longest Common Substrings of Minimum Length $k$ Between Genome Pairs
Year: 2024
Type: conference-paper
Abstract: A problem extension of the longest common sub-string (LCS) between two texts is the enumeration of all LCSs given a minimum length$k$(ALCS-k), along with their positions in each text. In bioinformatics, an efficient solution to the ALCS-$k$for very long texts -genomes or metagenomes- can provide useful insights to discover genetic signatures responsible for biological mechanisms. The ALCS-k problem has two additional requirements compared to the LCS problem: one is the minimum length$k$, and the other is that all common strings longer than$k$must be reported. We present an efficient, two-stage ALCS-k algorithm exploiting the spectrum of text substrings of length$k$(k-mers). Our approach yields a worst-case time complexity loglinear in the number of k-mers for the first stage, and an average-case loglinear in the number of common k-mers for the second stage (several orders of magnitudes smaller than the total k-mer spectrum). The space complexity is linear in the first phase (disk-based), and on average linear in the second phase (disk- and memory-based). Tests performed on genomes for different organisms (including viruses, bacteria and animal chromosomes) show that run times are consistent with our theoretical estimates; further, comparisons with MUMmer4 show an asymptotic advantage with divergent genomes.
Authors: Mattia Prosperi, Simone Marini, Christina Boucher
Institution: University of Florida
Language: English
Subfield: Artificial Intelligence
Field: Computer Science
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W4401754037