Search results for "LCP"

Detecting mutations by eBWT

2018

In this paper we develop a theory describing how the extended Burrows-Wheeler Transform (eBWT) of a collection of DNA fragments tends to cluster together the copies of nucleotides sequenced from a genome G. Our theory accurately predicts how many copies of any nucleotide are expected inside each such cluster, and how an elegant and precise LCP array based procedure can locate these clusters in the eBWT. Our findings are very general and can be applied to a wide range of different problems. In this paper, we consider the case of alignment-free and reference-free SNPs discovery in multiple collections of reads. We note that, in accordance with our theoretical results, SNPs are clustered in th…

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…

Linear-size suffix tries

2016

Suffix trees are highly regarded data structures for text indexing and string algorithms [MCreight 76, Weiner 73]. For any given string w of length n = | w | , a suffix tree for w takes O ( n ) nodes and links. It is often presented as a compacted version of a suffix trie for w, where the latter is the trie (or digital search tree) built on the suffixes of w. Here the compaction process replaces each maximal chain of unary nodes with a single arc. For this, the suffix tree requires that the labels of its arcs are substrings encoded as pointers to w (or equivalent information). On the contrary, the arcs of the suffix trie are labeled by single symbols but there can be Θ ( n 2 ) nodes and lin…

Fast Implementation of Double-coupled Nonnegative Canonical Polyadic Decomposition

2019

Real-world data exhibiting high order/dimensionality and various couplings are linked to each other since they share some common characteristics. Coupled tensor decomposition has become a popular technique for group analysis in recent years, especially for simultaneous analysis of multi-block tensor data with common information. To address the multiblock tensor data, we propose a fast double-coupled nonnegative Canonical Polyadic Decomposition (FDC-NCPD) algorithm in this study, based on the linked CP tensor decomposition (LCPTD) model and fast Hierarchical Alternating Least Squares (Fast-HALS) algorithm. The proposed FDCNCPD algorithm enables simultaneous extraction of common components, i…

Lightweight LCP construction for very large collections of strings

2016

The longest common prefix array is a very advantageous data structure that, combined with the suffix array and the Burrows-Wheeler transform, allows to efficiently compute some combinatorial properties of a string useful in several applications, especially in biological contexts. Nowadays, the input data for many problems are big collections of strings, for instance the data coming from "next-generation" DNA sequencing (NGS) technologies. In this paper we present the first lightweight algorithm (called extLCP) for the simultaneous computation of the longest common prefix array and the Burrows-Wheeler transform of a very large collection of strings having any length. The computation is reali…

Hormonal regulation of JP29 in the epidermis during Larval development and metamorphosis in the Tobacco Hornworm, Manduca sexta

1997

Docosahexaenoic acid, but not eicosapentaenoic acid, lowers ambulatory blood pressure and shortens interval QT in spontaneously hypertensive rats in …

2009

International audience; This study was designed to evaluate the effects of individual dietary long-chain n-3 polyunsaturated fatty acids (LCPUFA) on hypertension and cardiac consecutive disorders in spontaneously hypertensive rats (SHR) as compared to Wistar-Kyoto rats (WKY). Rats were fed for 2 months an eicosapentaenoic (EPA)- or docosahexaenoic acid (DHA)-rich diet (240 mg/day) or an n-3 PUFA-free diet. Male SHR (n=6), implanted with cardiovascular telemetry devices, were housed in individual cages for continuous measurements of cardiovascular parameters (blood pressure (BP) and heart rate (HR)) during either activity or rest periods, ECG were recorded during the quiet period. The n-6 PU…

Resource or waste? A perspective of plastics degradation in soil with a focus on end-of-life options.

2018

‘Capable-of-being-shaped’ synthetic compounds are prevailing today over horn, bone, leather, wood, stone, metal, glass, or ceramic in products that were previously left to natural materials. Plastic is, in fact, economical, simple, adaptable, and waterproof. Also, it is durable and resilient to natural degradation (although microbial species capable of degrading plastics do exist). In becoming a waste, plastic accumulation adversely affects ecosystems. The majority of plastic debris pollutes waters, accumulating in oceans. And, the behaviour and the quantity of plastic, which has become waste, are rather well documented in the water, in fact. This review collects existing information on pla…

Synthesis of PP-LCP graft copolymers and their compatibilizing activity for PP/LCP blends

1998

The aim of this work was the synthesis of new graft copolymers consisting of polypropylene (PP) backbones and liquid crystalline polymer (LCP) branches, to be used as compatibilizing agents for PP/LCP blends. The PP-g-LCP copolymers have been prepared by polycondensation of the monomers of a semiflexible liquid crystalline polyester (SBH 1 : 1 : 2), that is, sebacic acid (S), 4,4′-dihydroxybiphenyl (B), and 4-hydroxybenzoic acid (H) in the mole ratio of 1 : 1 : 2, carried out in the presence of appropriate amounts of a commercial acrylic-acid-functionalized polypropylene (PPAA). The polycondensation products, referred to as COPP50 and COPP70, having a calculated PPAA concentration of 50 and…

Use of PP-g-OXA in the Compatibilization of PP/LCP Blends

1999

Abstract Adding small amounts of liquid crystalline polymers (LCP) to flexible thermoplastic matrices (FTP) allows to enhance the mechanical and thermomechanical properties. Therefore it is possible to obtain materials with new properties only by simple mixing. A strong shortcoming is the incompatibility between LCP and FTP that leads to materials with very poor properties unusable for commercial pourposes. The presence of a compatibilizer is therefore required. Oxazoline functionality is known to be highly reactive toward many other functional groups and then oxazoline functionalized polymers can be efficiently used as compatibilizer precursors. In this work the compatibilizazion of polypr…