Document Type
Article
Publication Date
3-1-2013
Abstract
Let T=T1pk1T2pk2â̄ pkdTd+1 be a text of total length n, where characters of each Ti are chosen from an alphabet Σ of size σ, and p denotes a wildcard symbol. The text indexing with wildcards problem is to index T such that when we are given a query pattern P, we can locate the occurrences of P in T efficiently. This problem has been applied in indexing genomic sequences that contain single-nucleotide polymorphisms (SNP) because SNP can be modeled as wildcards. Recently Tam et al. (2009) and Thachuk (2011) have proposed succinct indexes for this problem. In this paper, we present the first compressed index for this problem, which takes only nHh+o(nlogσ )+O(dlogn) bits of space, where Hh is the hth-order empirical entropy (h=o(logσn)) of T. © 2012 Elsevier B.V.
Publication Source (Journal or Book title)
Journal of Discrete Algorithms
First Page
23
Last Page
29
Recommended Citation
Hon, W., Ku, T., Shah, R., Thankachan, S., & Vitter, J. (2013). Compressed text indexing with wildcards. Journal of Discrete Algorithms, 19, 23-29. https://doi.org/10.1016/j.jda.2012.12.003
