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pro vyhledávání: '"Cazaux, Bastien"'
The hierarchical overlap graph (HOG) is a graph that encodes overlaps from a given set P of n strings, as the overlap graph does. A best known algorithm constructs HOG in O(||P|| log n) time and O(||P||) space, where ||P|| is the sum of lengths of th
Externí odkaz:
http://arxiv.org/abs/2102.12824
Autor:
Equi, Massimo, Norri, Tuukka, Alanko, Jarno, Cazaux, Bastien, Tomescu, Alexandru I., Mäkinen, Veli
We study the problem of matching a string in a labeled graph. Previous research has shown that unless the Orthogonal Vectors Hypothesis (OVH) is false, one cannot solve this problem in strongly sub-quadratic time, nor index the graph in polynomial ti
Externí odkaz:
http://arxiv.org/abs/2102.12822
Autor:
Cazaux, Bastien, Rivals, Eric
A superstring of a set of strings correspond to a string which contains all the other strings as substrings. The problem of finding the Shortest Linear Superstring is a well-know and well-studied problem in stringology. We present here a variant of t
Externí odkaz:
http://arxiv.org/abs/2012.08878
We introduce a compact pangenome representation based on an optimal segmentation concept that aims to reconstruct founder sequences from a multiple sequence alignment (MSA). Such founder sequences have the feature that each row of the MSA is a recomb
Externí odkaz:
http://arxiv.org/abs/2005.09342
Autor:
Cazaux, Bastien
Actuellement, les technologies de séquençage ne permettent de lire la séquence d'un génome entier d'un individu, mais donnent les séquences de portions courtes de ce génome avec des erreurs. On doit ensuite procéder à un assemblage de ces sé
Externí odkaz:
http://www.theses.fr/2016MONTT307/document
Akademický článek
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Autor:
Cazaux, Bastien, Rivals, Eric
Publikováno v:
30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019), Leibniz International Proceedings in Informatics (LIPIcs), vol 128, p. 24:1--24:20, 2019
The boom of genomic sequencing makes compression of set of sequences inescapable. This underlies the need for multi-string indexing data structures that helps compressing the data. The most prominent example of such data structures is the Burrows-Whe
Externí odkaz:
http://arxiv.org/abs/1805.10070
Publikováno v:
In Proc. WABI 2018
Given a threshold $L$ and a set $\mathcal{R} = \{R_1, \ldots, R_m\}$ of $m$ haplotype sequences, each having length $n$, the minimum segmentation problem for founder reconstruction is to partition the sequences into disjoint segments $\mathcal{R}[i_1
Externí odkaz:
http://arxiv.org/abs/1805.03574
Autor:
Cazaux, Bastien, Rivals, Eric
Publikováno v:
Information Processing Letters Volume 155, March 2020, 105862
Given a set of finite words, the Overlap Graph (OG) is a complete weighted digraph where each word is a node and where the weight of an arc equals the length of the longest overlap of one word onto the other (Overlap is an asymmetric notion). The OG
Externí odkaz:
http://arxiv.org/abs/1802.04632
For analysing text algorithms, for computing superstrings, or for testing random number generators, one needs to compute all overlaps between any pairs of words in a given set. The positions of overlaps of a word onto itself, or of two words, are nee
Externí odkaz:
http://arxiv.org/abs/1707.05613