Zobrazeno 1 - 10
of 13
pro vyhledávání: '"Heuristic Alignment Procedure"'
Autor:
Vladimir Smirnov
Publikováno v:
PLoS Computational Biology
PLoS Computational Biology, Vol 17, Iss 10, p e1008950 (2021)
PLoS Computational Biology, Vol 17, Iss 10, p e1008950 (2021)
Multiple sequence alignment tools struggle to keep pace with rapidly growing sequence data, as few methods can handle large datasets while maintaining alignment accuracy. We recently introduced MAGUS, a new state-of-the-art method for aligning large
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3f936ecba0b302713fb63eb3397138d9
https://doi.org/10.1101/2021.04.09.439137
https://doi.org/10.1101/2021.04.09.439137
Publikováno v:
PLoS Computational Biology
PLoS Computational Biology, Vol 13, Iss 6, p e1005420 (2017)
PLoS Computational Biology, Vol 13, Iss 6, p e1005420 (2017)
Circular RNA (circRNA) is mainly generated by the splice donor of a downstream exon joining to an upstream splice acceptor, a phenomenon known as backsplicing. It has been reported that circRNA can function as microRNA (miRNA) sponges, transcriptiona
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::af943e037d561c5b214f4f73eead86ff
http://europepmc.org/articles/PMC6527241
http://europepmc.org/articles/PMC6527241
Publikováno v:
PLoS ONE, Vol 14, Iss 1, p e0209712 (2019)
PLoS ONE
PLoS ONE
The use of variable-length genomes in evolutionary computation has applications in optimisation when the size of the search space is unknown, and provides a unique environment to study the evolutionary dynamics of genome structure. Here, we revisit c
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d32ca320f356522ab269d0f557dcc9f3
https://doaj.org/article/3299757fc9384021a9c3ed600e95b542
https://doaj.org/article/3299757fc9384021a9c3ed600e95b542
Publikováno v:
PLoS ONE, Vol 14, Iss 1, p e0210177 (2019)
PLoS ONE
PLoS ONE
Protein structure alignment is an important tool for studying evolutionary biology and protein modeling. A tool which intensively searches for the globally optimal non-sequential alignments is rarely found. We propose ALIGN-CSA which shows improvemen
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5e24234f07691c242a4269b99193dc96
https://doaj.org/article/a693dfcab79d4f95b5f2628618224daf
https://doaj.org/article/a693dfcab79d4f95b5f2628618224daf
Autor:
Mark Chaisson, Jingwen Ren
Publikováno v:
PLoS Computational Biology
PLoS Computational Biology, Vol 17, Iss 6, p e1009078 (2021)
PLoS Computational Biology, Vol 17, Iss 6, p e1009078 (2021)
It is computationally challenging to detect variation by aligning single-molecule sequencing (SMS) reads, or contigs from SMS assemblies. One approach to efficiently align SMS reads is sparse dynamic programming (SDP), where optimal chains of exact m
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::11dfc23cee01f60d8723bf066828f54e
https://doi.org/10.1371/journal.pcbi.1009078
https://doi.org/10.1371/journal.pcbi.1009078
Autor:
Wan Fokkink, Sanne Abeln, Punto Bawono, Jaap Heringa, K. Anton Feenstra, Maurits J. J. Dijkstra
Publikováno v:
PLoS Computational Biology, Vol 14, Iss 11, p e1006547 (2018)
PLoS Computational Biology
PLoS Computational Biology, 14(11):e1006547. Public Library of Science
PLoS Computational Biology
PLoS Computational Biology, 14(11):e1006547. Public Library of Science
Protein or DNA motifs are sequence regions which possess biological importance. These regions are often highly conserved among homologous sequences. The generation of multiple sequence alignments (MSAs) with a correct alignment of the conserved seque
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1d8bf5fada7ff59ae7859ecd3bcc841b
https://doi.org/10.1371/journal.pcbi.1006547
https://doi.org/10.1371/journal.pcbi.1006547
Publikováno v:
PLoS ONE
PLoS ONE, Vol 13, Iss 2, p e0192987 (2018)
PLoS ONE, Vol 13, Iss 2, p e0192987 (2018)
In this paper, we propose a connectivity-preserving flocking algorithm for multi-agent systems in which the neighbor set of each agent is determined by the hybrid metric-topological distance so that the interaction topology can be represented as the
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cf19194a7b9fe5d38ad830e84e4ca6fd
http://europepmc.org/articles/PMC5819810
http://europepmc.org/articles/PMC5819810
Publikováno v:
PLoS ONE, Vol 13, Iss 8, p e0200815 (2018)
PLoS ONE
PLoS ONE
The sequence space of five protein superfamilies was investigated by constructing sequence networks. The nodes represent individual sequences, and two nodes are connected by an edge if the global sequence identity of two sequences exceeds a threshold
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid_dedup__::92e2fa3b6d98a0442c93a90010fc38e3
http://europepmc.org/articles/PMC6070207?pdf=render
http://europepmc.org/articles/PMC6070207?pdf=render
Publikováno v:
PLoS ONE, Vol 11, Iss 11, p e0166177 (2016)
PLoS ONE
PLoS ONE
Potamogeton is one of the most difficult groups to clarify in aquatic plants, which has an extensive range of interspecific morphological and ecological diversity. Internal transcribed spacer (ITS) is prevalent for phylogenetic analysis in plants. Ho
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fdf657684f5cbc31a63f3325c78316c2
https://pubmed.ncbi.nlm.nih.gov/36584071
https://pubmed.ncbi.nlm.nih.gov/36584071
Autor:
Vincent Ranwez
Publikováno v:
Plos One 8 (11), . (2016)
PLoS ONE, Vol 11, Iss 8, p e0160043 (2016)
PLoS ONE
PLoS ONE, Public Library of Science, 2016, 11 (8), ⟨10.1371/journal.pone.0160043⟩
PLoS ONE, Vol 11, Iss 8, p e0160043 (2016)
PLoS ONE
PLoS ONE, Public Library of Science, 2016, 11 (8), ⟨10.1371/journal.pone.0160043⟩
BACKGROUND: Multiple sequence alignment (MSA) is a crucial step in many molecular analyses and many MSA tools have been developed. Most of them use a greedy approach to construct a first alignment that is then refined by optimizing the sum of pair sc
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::15971fdd8405f49f5bad1a11ef809d06
http://prodinra.inra.fr/record/368160
http://prodinra.inra.fr/record/368160