Zobrazeno 1 - 10
of 30
pro vyhledávání: '"Fabio Cunial"'
Autor:
Victoria Popic, Chris Rohlicek, Fabio Cunial, Iman Hajirasouliha, Dmitry Meleshko, Kiran Garimella, Anant Maheshwari
Publikováno v:
Nature Methods. 20:559-568
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::86a1c28b7a59b20438a85aed047b98ed
https://doi.org/10.1038/s41592-023-01799-x
https://doi.org/10.1038/s41592-023-01799-x
Publikováno v:
Bioinformatics (Oxford, England).
Motivation Fast, lightweight methods for comparing the sequence of ever larger assembled genomes from ever growing databases are increasingly needed in the era of accurate long reads and pan-genome initiatives. Matching statistics is a popular method
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4b0c839f4cbd37678a4cb03b5b7e5109
https://pubmed.ncbi.nlm.nih.gov/35134833
https://pubmed.ncbi.nlm.nih.gov/35134833
Publikováno v:
Bioinformatics. 35:4607-4616
Motivation Markov models with contexts of variable length are widely used in bioinformatics for representing sets of sequences with similar biological properties. When models contain many long contexts, existing implementations are either unable to h
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3a67f3af93fd8d159a9ad5eec8dff3c9
https://doi.org/10.1093/bioinformatics/btz268
https://doi.org/10.1093/bioinformatics/btz268
Autor:
Djamal Belazzougui, Fabio Cunial
Publikováno v:
String Processing and Information Retrieval ISBN: 9783030592110
SPIRE
SPIRE
Burrows-Wheeler indexes that support both extending and contracting any substring of the text T of length n on which they are built, in any direction, provide substantial flexibility in traversing the text and can be used to implement several algorit
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::003a140f87791c20e9fb055fa079323e
https://doi.org/10.1007/978-3-030-59212-7_4
https://doi.org/10.1007/978-3-030-59212-7_4
Autor:
Fabio Cunial, Djamal Belazzougui
Publikováno v:
String Processing and Information Retrieval ISBN: 9783319674278
SPIRE
SPIRE
The compact directed acyclic word graph (CDAWG) of a string T of length n takes space proportional just to the number e of right extensions of the maximal repeats of T, and it is thus an appealing index for highly repetitive datasets, like collection
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::f714e12b1621f6b1880b39cc205f81d6
https://doi.org/10.1007/978-3-319-67428-5_14
https://doi.org/10.1007/978-3-319-67428-5_14
The field of succinct data structures has flourished over the last 16 years. Starting from the compressed suffix array (CSA) by Grossi and Vitter (STOC 2000) and the FM-index by Ferragina and Manzini (FOCS 2000), a number of generalizations and appli
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::80dc97cd5c450a1900c49ca4934eefae
http://arxiv.org/abs/1609.06378
http://arxiv.org/abs/1609.06378
Autor:
Alberto Apostolico, Fabio Cunial
Publikováno v:
Encyclopedia of Algorithms ISBN: 9783642278488
Encyclopedia of Algorithms
Encyclopedia of Algorithms
The suffix tree is one of the oldest full-text inverted indexes and one of the most persistent subjects of study in the theory of algorithms. With extensions and refinements, including succinct and compressed variants that provide some of its express
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::18ced5900966a448187562ebb01b9e0e
https://doi.org/10.1007/978-1-4939-2864-4_627
https://doi.org/10.1007/978-1-4939-2864-4_627
Autor:
Alberto Apostolico, Fabio Cunial
Publikováno v:
Journal of computational biology 19 (2012): 911–927.
info:cnr-pdr/source/autori:Alberto Apostolico, Fabio Cunial/titolo:Phylogeny Construction with Rigid Gapped Motifs/doi:/rivista:Journal of computational biology/anno:2012/pagina_da:911/pagina_a:927/intervallo_pagine:911–927/volume:19
info:cnr-pdr/source/autori:Alberto Apostolico, Fabio Cunial/titolo:Phylogeny Construction with Rigid Gapped Motifs/doi:/rivista:Journal of computational biology/anno:2012/pagina_da:911/pagina_a:927/intervallo_pagine:911–927/volume:19
Patterns with gaps have traditionally been used as signatures of protein families or as features in binary classification. Current alignment-free algorithms construct phylogenies by comparing the repertoire and frequency of ungapped blocks in genomes
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c1e95a072e04fc96a03ead86c18a2785
https://doi.org/10.1089/cmb.2012.0060
https://doi.org/10.1089/cmb.2012.0060
Autor:
Alberto Apostolico, Fabio Cunial
Publikováno v:
Journal of Computational Biology. 17:1011-1049
The quantitative underpinning of the information content of biosequences represents an elusive goal and yet also an obvious prerequisite to the quantitative modeling and study of biological function and evolution. Several past studies have addressed
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::baa6a1cd558d71e81c08780f47a391b7
https://doi.org/10.1089/cmb.2010.0073
https://doi.org/10.1089/cmb.2010.0073
Autor:
Fabio Cunial, Alberto Apostolico
Publikováno v:
Theoretical Computer Science. 410(43):4360-4371
Words that appear as constrained subsequences in a text-string are considered as possible indicators of the host string structure, hence also as a possible means of sequence comparison and classification. The constraint consists of imposing a bound o
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::417302e84fbc2a198e5cbab6d6ec5d85