2,569 research outputs found
Broadword Implementation of Parenthesis Queries
We continue the line of research started in "Broadword Implementation of
Rank/Select Queries" proposing broadword (a.k.a. SWAR, "SIMD Within A
Register") algorithms for finding matching closed parentheses and the k-th far
closed parenthesis. Our algorithms work in time O(log w) on a word of w bits,
and contain no branch and no test instruction. On 64-bit (and wider)
architectures, these algorithms make it possible to avoid costly tabulations,
while providing a very significant speedup with respect to for-loop
implementations
Simple and Efficient Fully-Functional Succinct Trees
The fully-functional succinct tree representation of Navarro and Sadakane
(ACM Transactions on Algorithms, 2014) supports a large number of operations in
constant time using bits. However, the full idea is hard to
implement. Only a simplified version with operation time has been
implemented and shown to be practical and competitive. We describe a new
variant of the original idea that is much simpler to implement and has
worst-case time for the operations. An implementation based on
this version is experimentally shown to be superior to existing
implementations
Prospects and limitations of full-text index structures in genome analysis
The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared
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