Mar 9, 2020 · Deterministic linear time is achieved by exploiting a new partial rank data structure that supports queries in constant time and that might have ...

Sep 20, 2016 · We report the following advances in string indexing and analysis. We show that the BWT of a string T\in \{1,\ldots,\sigma\}^n can be built in deterministic O(n ...

In Section 6, we will describe algorithms for building the compressed suffix array, the BWT index, and the succinct suffix array, in deterministic linear time ...

For example, one can compare two genomes by building a common index for their concatenation and by detecting common substructures by querying the index.

... iGenomics uses a version of QuickSort, a divide-and-conquer sorting algorithm, because on average it takes O(n log n) time for n objects to be sorted.

Belazzougui, Djamal ; Cunial, Fabio ; Karkkainen, Juha et al. / Linear-time String Indexing and Analysis in Small Space. In: ACM Transactions on Algorithms.

Linear-time String Indexing and Analysis in Small Space · Djamal Belazzougui: University of Helsinki, Helsinki, Finland · Fabio Cunial · Juha Kärkkäinen · Veli ...

Our main contribution is a space-time trade-off for the Internal Pattern Matching (IPM) problem, where the goal is to construct a data structure over a string S ...

Our main result is a novel linear space data structure that achieves near-optimal query time for patterns compressed with the classic Lempel-Ziv 1977 (LZ77).

For small strings (|S′| ≤ w1/5) we pick a hash function from Σ → [0, w/ log w] that is injective with (almost) high probability, and use this to manually ...