Subset Wavelet Trees
| Autor: | Alanko, Jarno N., Biagi, Elena, Puglisi, Simon J., Vuohtoniemi, Jaakko |
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| Jazyk: | angličtina |
| Rok vydání: | 2023 |
| Předmět: | |
| DOI: | 10.4230/lipics.sea.2023.4 |
| Popis: | Given an alphabet Σ of σ = |Σ| symbols, a degenerate (or indeterminate) string X is a sequence X = X[0],X[1]…, X[n-1] of n subsets of Σ. Since their introduction in the mid 70s, degenerate strings have been widely studied, with applications driven by their being a natural model for sequences in which there is a degree of uncertainty about the precise symbol at a given position, such as those arising in genomics and proteomics. In this paper we introduce a new data structural tool for degenerate strings, called the subset wavelet tree (SubsetWT). A SubsetWT supports two basic operations on degenerate strings: subset-rank(i,c), which returns the number of subsets up to the i-th subset in the degenerate string that contain the symbol c; and subset-select(i,c), which returns the index in the degenerate string of the i-th subset that contains symbol c. These queries are analogs of rank and select queries that have been widely studied for ordinary strings. Via experiments in a real genomics application in which degenerate strings are fundamental, we show that subset wavelet trees are practical data structures, and in particular offer an attractive space-time tradeoff. Along the way we investigate data structures for supporting (normal) rank queries on base-4 and base-3 sequences, which may be of independent interest. Our C++ implementations of the data structures are available at https://github.com/jnalanko/SubsetWT. LIPIcs, Vol. 265, 21st International Symposium on Experimental Algorithms (SEA 2023), pages 4:1-4:14 |
| Databáze: | OpenAIRE |
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