Dictionary Matching in Elastic-Degenerate Texts with Applications in Searching VCF Files On-line

Abstract

An elastic-degenerate string is a sequence of n sets of strings of total length N . It has been introduced to represent multiple sequence alignments of closely-related sequences in a compact form. For a standard pattern of length m, pattern matching in an elastic-degenerate text can be solved on-line in time O(nm2 +N) with pre-processing time and space O(m) (Grossi et al., CPM 2017). A fast bit-vector algorithm requiring time O(N · dmw e) with pre-processing time and space O(m·dmw e), where w is the size of the computer word, was also presented. In this paper we consider the same problem for a set of patterns of total length M . A straightforward generalization of the existing bit-vector algorithm would require time O(N · dMw e) with pre-processing time and space O(M · dMw e), which is prohibitive in practice. We present a new on-line O(N · d M w e)-time algorithm with pre-processing time and space O(M). We present experimental results using both synthetic and real data demonstrating the performance of the algorithm. We further demonstrate a real application of our algorithm in a pipeline for discovery and verification of minimal absent words (MAWs) in the human genome showing that a significant number of previously discovered MAWs are in fact false-positives when a population’s variants are considered. 2012 ACM Subject Classification Theory of computation → Pattern matching