Zobrazeno 1 - 10
of 64
pro vyhledávání: '"Felipe A. Louza"'
Publikováno v:
BMC Bioinformatics, Vol 21, Iss S8, Pp 1-25 (2020)
Abstract Background The development of Next Generation Sequencing (NGS) has had a major impact on the study of genetic sequences. Among problems that researchers in the field have to face, one of the most challenging is the taxonomic classification o
Externí odkaz:
https://doaj.org/article/0a21ed84c0734c7bb82f1a2e1a0601f0
Publikováno v:
Algorithms for Molecular Biology, Vol 15, Iss 1, Pp 1-5 (2020)
Abstract Background The construction of a suffix array for a collection of strings is a fundamental task in Bioinformatics and in many other applications that process strings. Related data structures, as the Longest Common Prefix array, the Burrows
Externí odkaz:
https://doaj.org/article/5cf5db694d514e1eab49f2be29d24638
Autor:
Marcelo K. Albertini, Felipe A. Louza
Publikováno v:
Mathematics, Vol 11, Iss 1, p 139 (2022)
We evaluate the influence of different alphabet orderings on the Lyndon factorization of a string. Experiments with Pizza&Chili datasets show that for most alphabet reorderings, the number of Lyndon factors is usually small, and the length of the lon
Externí odkaz:
https://doaj.org/article/dd343d33191a4540ad4fcde86ae0bae4
Publikováno v:
Algorithms for Molecular Biology, Vol 14, Iss 1, Pp 1-15 (2019)
Abstract Background Sequencing technologies produce larger and larger collections of biosequences that have to be stored in compressed indices supporting fast search operations. Many compressed indices are based on the Burrows–Wheeler Transform (BW
Externí odkaz:
https://doaj.org/article/2ec00b4a05644bf9af467fff8f8b094a
Publikováno v:
Algorithms for Molecular Biology, Vol 12, Iss 1, Pp 1-16 (2017)
Abstract Background Suffix arrays, augmented by additional data structures, allow solving efficiently many string processing problems. The external memory construction of the generalized suffix array for a string collection is a fundamental task when
Externí odkaz:
https://doaj.org/article/bc8337213dc2403ea213db794ca99cb2
The merging of succinct data structures is a well established technique for the space efficient construction of large succinct indexes. In the first part of the paper we propose a new algorithm for merging succinct representations of de Bruijn graphs
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3a1d4763f8c39254924ca8cbf8769bc0
http://hdl.handle.net/11568/1105890
http://hdl.handle.net/11568/1105890
Publikováno v:
Repositório Institucional da USP (Biblioteca Digital da Produção Intelectual)
Universidade de São Paulo (USP)
instacron:USP
Universidade de São Paulo (USP)
instacron:USP
The Burrows-Wheeler transform (BWT) is a well studied text transformation widely used in data compression and text indexing. The BWT of two strings can also provide similarity measures between them, based on the observation that the more their symbol
A grammar compression algorithm, called GCIS, is introduced in this work. GCIS is based on the induced suffix sorting algorithm SAIS, presented by Nong et al. in 2009. The proposed solution builds on the factorization performed by SAIS during suffix
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5952cf547e8c5728a6cbd4afacf3e59b
http://arxiv.org/abs/2011.12898
http://arxiv.org/abs/2011.12898
Publikováno v:
Algorithms for Molecular Biology : AMB
Algorithms for Molecular Biology, Vol 15, Iss 1, Pp 1-5 (2020)
Algorithms for Molecular Biology, Vol 15, Iss 1, Pp 1-5 (2020)
Background The construction of a suffix array for a collection of strings is a fundamental task in Bioinformatics and in many other applications that process strings. Related data structures, as the Longest Common Prefix array, the Burrows–Wheeler
In this paper we propose a new, more appropriate definition of regular and indeterminate strings. A regular string is one that is "isomorphic" to a string whose entries all consist of a single letter, but which nevertheless may itself include entries
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6fc826f498dfd3eb04c1c8dd56ea41fc