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of 173
pro vyhledávání: '"Pisanti Nadia"'
In this paper, we introduce flubbles, a new definition of "bubbles" corresponding to variants in a (pan)genome graph $G$. We then show a characterization for flubbles in terms of equivalence classes regarding cycles in an intermediate data structure
Externí odkaz:
http://arxiv.org/abs/2410.20932
In recent years, aligning a sequence to a pangenome has become a central problem in genomics and pangenomics. A fast and accurate solution to this problem can serve as a toolkit to many crucial tasks such as read-correction, Multiple Sequences Alignm
Externí odkaz:
http://arxiv.org/abs/2206.03242
Autor:
Charalampopoulos, Panagiotis, Chen, Huiping, Christen, Peter, Loukides, Grigorios, Pisanti, Nadia, Pissis, Solon P., Radoszewski, Jakub
In the Pattern Masking for Dictionary Matching (PMDM) problem, we are given a dictionary $\mathcal{D}$ of $d$ strings, each of length $\ell$, a query string $q$ of length $\ell$, and a positive integer $z$, and we are asked to compute a smallest set
Externí odkaz:
http://arxiv.org/abs/2006.16137
Publikováno v:
Algorithms for Molecular Biology, Vol 4, Iss 1, p 3 (2009)
Abstract Background Identifying local similarity between two or more sequences, or identifying repeats occurring at least twice in a sequence, is an essential part in the analysis of biological sequences and of their phylogenetic relationship. Findin
Externí odkaz:
https://doaj.org/article/87d767d958ee4bca8b156142e444e32d
Autor:
Bernardini, Giulia, Chen, Huiping, Conte, Alessio, Grossi, Roberto, Loukides, Grigorios, Pisanti, Nadia, Pissis, Solon P., Rosone, Giovanna, Sweering, Michelle
String data are often disseminated to support applications such as location-based service provision or DNA sequence analysis. This dissemination, however, may expose sensitive patterns that model confidential knowledge. In this paper, we consider the
Externí odkaz:
http://arxiv.org/abs/1906.11030
An elastic-degenerate (ED) string is a sequence of $n$ sets of strings of total length $N$, which was recently proposed to model a set of similar sequences. The ED string matching (EDSM) problem is to find all occurrences of a pattern of length $m$ i
Externí odkaz:
http://arxiv.org/abs/1905.02298
Autor:
Ayad, Lorraine A. K, Bernardini, Giulia, Grossi, Roberto, Iliopoulos, Costas S., Pisanti, Nadia, Pissis, Solon P., Rosone, Giovanna
In this paper we introduce a new family of string processing problems. We are given two or more strings and we are asked to compute a factor common to all strings that preserves a specific property and has maximal length. Here we consider three funda
Externí odkaz:
http://arxiv.org/abs/1810.02099
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 cop
Externí odkaz:
http://arxiv.org/abs/1805.01876
Akademický článek
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Autor:
Ferreira, Rui, Grossi, Roberto, Marino, Andrea, Pisanti, Nadia, Rizzi, Romeo, Sacomoto, Gustavo
We present the first optimal algorithm for the classical problem of listing all the cycles in an undirected graph. We exploit their properties so that the total cost is the time taken to read the input graph plus the time to list the output, namely,
Externí odkaz:
http://arxiv.org/abs/1205.2766