Search results for "Burrows"

Estimating the abundance of burrow-nesting species through the statistical analysis of combined playback and visual surveys

2016

Like night and day: Reversals of thermal gradients across ghost crab burrows and their implications for thermal ecology

2018

Abstract Ghost crabs, Ocypode cordimanus, inhabit relatively hostile environments subject to thermal fluctuations, including both diurnal and seasonal cycles. For many ectotherms, including ghost crabs, a major challenge is to remain cool during hot daytime temperatures. This can be achieved by adopting a fossorial lifestyle, taking advantage of thermal refuge afforded by burrows of sufficient depth. Another consideration, often overlooked, is the potential advantage associated with ready access to a thermal energy source (a “charging station”) when surface temperatures are cooler. Being able to rapidly elevate body temperature during cool periods would enhance the crab's ability to maintai…

The colored longest common prefix array computed via sequential scans

2018

Due to the increased availability of large datasets of biological sequences, the tools for sequence comparison are now relying on efficient alignment-free approaches to a greater extent. Most of the alignment-free approaches require the computation of statistics of the sequences in the dataset. Such computations become impractical in internal memory when very large collections of long sequences are considered. In this paper, we present a new conceptual data structure, the colored longest common prefix array (cLCP), that allows to efficiently tackle several problems with an alignment-free approach. In fact, we show that such a data structure can be computed via sequential scans in semi-exter…

Parallel and Space-Efficient Construction of Burrows-Wheeler Transform and Suffix Array for Big Genome Data

2016

Next-generation sequencing technologies have led to the sequencing of more and more genomes, propelling related research into the era of big data. In this paper, we present ParaBWT, a parallelized Burrows-Wheeler transform (BWT) and suffix array construction algorithm for big genome data. In ParaBWT, we have investigated a progressive construction approach to constructing the BWT of single genome sequences in linear space complexity, but with a small constant factor. This approach has been further parallelized using multi-threading based on a master-slave coprocessing model. After gaining the BWT, the suffix array is constructed in a memory-efficient manner. The performance of ParaBWT has b…

Computing the Original eBWT Faster, Simpler, and with Less Memory

2021

Mantaci et al. [TCS 2007] defined the \(\mathrm {eBWT}\) to extend the definition of the \(\mathrm {BWT}\) to a collection of strings. However, since this introduction, it has been used more generally to describe any \(\mathrm {BWT}\) of a collection of strings, and the fundamental property of the original definition (i.e., the independence from the input order) is frequently disregarded. In this paper, we propose a simple linear-time algorithm for the construction of the original \(\mathrm {eBWT}\), which does not require the preprocessing of Bannai et al. [CPM 2021]. As a byproduct, we obtain the first linear-time algorithm for computing the \(\mathrm {BWT}\) of a single string that uses …

The Myriad Virtues of Wavelet Trees

2009

Wavelet Trees have been introduced in [Grossi, Gupta and Vitter, SODA '03] and have been rapidly recognized as a very flexible tool for the design of compressed full-text indexes and data compressors. Although several papers have investigated the beauty and usefulness of this data structure in the full-text indexing scenario, its impact on data compression has not been fully explored. In this paper we provide a complete theoretical analysis of a wide class of compression algorithms based on Wavelet Trees. We also show how to improve their asymptotic performance by introducing a novel framework, called Generalized Wavelet Trees, that aims for the best combination of binary compressors (like,…

Combinatorial Transforms : Application in Lossless Image Compression

2011

International audience; Common image compression standards are usually based on frequency transform such as Discrete Cosine Transform. We present a different approach for lossless image compression, which is based on a combinatorial transform. The main transform is Burrows Wheeler Transform (BWT) which tends to reorder symbols according to their following context. It becomes one of promising compression approach based on context modeling. BWT was initially applied for text compression software such as BZIP2 nevertheless it has been recently applied to the image compression field. Compression schemes based on the Burrows Wheeler Transform have been usually lossless; therefore we implement th…

Variable-order reference-free variant discovery with the Burrows-Wheeler Transform

2020

Abstract Background In [Prezza et al., AMB 2019], a new reference-free and alignment-free framework for the detection of SNPs was suggested and tested. The framework, based on the Burrows-Wheeler Transform (BWT), significantly improves sensitivity and precision of previous de Bruijn graphs based tools by overcoming several of their limitations, namely: (i) the need to establish a fixed value, usually small, for the order k, (ii) the loss of important information such as k-mer coverage and adjacency of k-mers within the same read, and (iii) bad performance in repeated regions longer than k bases. The preliminary tool, however, was able to identify only SNPs and it was too slow and memory con…

Burrows–Wheeler transform and Sturmian words

2003

Burrows-Wheeler transform and palindromic richness

2009

AbstractThe investigation of the extremal case of the Burrows–Wheeler transform leads to study the words w over an ordered alphabet A={a1,a2,…,ak}, with a1<a2<⋯<ak, such that bwt(w) is of the form aknkak−1nk−1⋯a2n2a1n1, for some non-negative integers n1,n2,…,nk. A characterization of these words in the case |A|=2 has been given in [Sabrina Mantaci, Antonio Restivo, Marinella Sciortino, Burrows-Wheeler transform and Sturmian words, Information Processing Letters 86 (2003) 241–246], where it is proved that they correspond to the powers of conjugates of standard words. The case |A|=3 has been settled in [Jamie Simpson, Simon J. Puglisi, Words with simple Burrows-Wheeler transforms, Electronic …