8,038 research outputs found
Clustering words
We characterize words which cluster under the Burrows-Wheeler transform as
those words such that occurs in a trajectory of an interval exchange
transformation, and build examples of clustering words
Universal lossless source coding with the Burrows Wheeler transform
The Burrows Wheeler transform (1994) is a reversible sequence transformation used in a variety of practical lossless source-coding algorithms. In each, the BWT is followed by a lossless source code that attempts to exploit the natural ordering of the BWT coefficients. BWT-based compression schemes are widely touted as low-complexity algorithms giving lossless coding rates better than those of the Ziv-Lempel codes (commonly known as LZ'77 and LZ'78) and almost as good as those achieved by prediction by partial matching (PPM) algorithms. To date, the coding performance claims have been made primarily on the basis of experimental results. This work gives a theoretical evaluation of BWT-based coding. The main results of this theoretical evaluation include: (1) statistical characterizations of the BWT output on both finite strings and sequences of length n → ∞, (2) a variety of very simple new techniques for BWT-based lossless source coding, and (3) proofs of the universality and bounds on the rates of convergence of both new and existing BWT-based codes for finite-memory and stationary ergodic sources. The end result is a theoretical justification and validation of the experimentally derived conclusions: BWT-based lossless source codes achieve universal lossless coding performance that converges to the optimal coding performance more quickly than the rate of convergence observed in Ziv-Lempel style codes and, for some BWT-based codes, within a constant factor of the optimal rate of convergence for finite-memory source
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
Lyndon Array Construction during Burrows-Wheeler Inversion
In this paper we present an algorithm to compute the Lyndon array of a string
of length as a byproduct of the inversion of the Burrows-Wheeler
transform of . Our algorithm runs in linear time using only a stack in
addition to the data structures used for Burrows-Wheeler inversion. We compare
our algorithm with two other linear-time algorithms for Lyndon array
construction and show that computing the Burrows-Wheeler transform and then
constructing the Lyndon array is competitive compared to the known approaches.
We also propose a new balanced parenthesis representation for the Lyndon array
that uses bits of space and supports constant time access. This
representation can be built in linear time using words of space, or in
time using asymptotically the same space as
On the combinatorics of suffix arrays
We prove several combinatorial properties of suffix arrays, including a
characterization of suffix arrays through a bijection with a certain
well-defined class of permutations. Our approach is based on the
characterization of Burrows-Wheeler arrays given in [1], that we apply by
reducing suffix sorting to cyclic shift sorting through the use of an
additional sentinel symbol. We show that the characterization of suffix arrays
for a special case of binary alphabet given in [2] easily follows from our
characterization. Based on our results, we also provide simple proofs for the
enumeration results for suffix arrays, obtained in [3]. Our approach to
characterizing suffix arrays is the first that exploits their relationship with
Burrows-Wheeler permutations
On Bijective Variants of the Burrows-Wheeler Transform
The sort transform (ST) is a modification of the Burrows-Wheeler transform
(BWT). Both transformations map an arbitrary word of length n to a pair
consisting of a word of length n and an index between 1 and n. The BWT sorts
all rotation conjugates of the input word, whereas the ST of order k only uses
the first k letters for sorting all such conjugates. If two conjugates start
with the same prefix of length k, then the indices of the rotations are used
for tie-breaking. Both transforms output the sequence of the last letters of
the sorted list and the index of the input within the sorted list. In this
paper, we discuss a bijective variant of the BWT (due to Scott), proving its
correctness and relations to other results due to Gessel and Reutenauer (1993)
and Crochemore, Desarmenien, and Perrin (2005). Further, we present a novel
bijective variant of the ST.Comment: 15 pages, presented at the Prague Stringology Conference 2009 (PSC
2009
String attractors and combinatorics on words
The notion of string attractor has recently been introduced in [Prezza, 2017] and studied in [Kempa and Prezza, 2018] to provide a unifying framework for known dictionary-based compressors. A string attractor for a word w = w[1]w[2] · · · w[n] is a subset Γ of the positions 1, . . ., n, such that all distinct factors of w have an occurrence crossing at least one of the elements of Γ. While finding the smallest string attractor for a word is a NP-complete problem, it has been proved in [Kempa and Prezza, 2018] that dictionary compressors can be interpreted as algorithms approximating the smallest string attractor for a given word. In this paper we explore the notion of string attractor from a combinatorial point of view, by focusing on several families of finite words. The results presented in the paper suggest that the notion of string attractor can be used to define new tools to investigate combinatorial properties of the words
Aspherical supernova explosions and formation of compact black hole low-mass X-ray binaries
It has been suggested that black-hole low-mass X-ray binaries (BHLMXBs) with
short orbital periods may have evolved from BH binaries with an
intermediate-mass secondary, but the donor star seems to always have higher
effective temperatures than measured in BHLMXBs (Justham, Rappaport &
Podsiadlowski 2006). Here we suggest that the secondary star is originally an
intermediate-mass (\sim 2-5 M_{\sun}) star, which loses a large fraction of
its mass due to the ejecta impact during the aspherical SN explosion that
produced the BH. The resulted secondary star could be of low-mass (\la 1
M_{\sun}). Magnetic braking would shrink the binary orbit, drive mass transfer
between the donor and the BH, producing a compact BHLMXB.Comment: 4 pages, accepted for publication in MNRAS Letter
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