PairMotif: A new pattern-driven algorithm for planted (l, d) DNA motif search.

Motif search is a fundamental problem in bioinformatics with an important application in locating transcription factor binding sites (TFBSs) in DNA sequences. The exact algorithms can report all (l, d) motifs and find the best one under a specific objective function. However, it is still a challengi...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Qiang Yu, Hongwei Huo, Yipu Zhang, Hongzhi Guo
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f23df5d3df90474c820280cc1b2055be
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:f23df5d3df90474c820280cc1b2055be
record_format	dspace
spelling	oai:doaj.org-article:f23df5d3df90474c820280cc1b2055be2021-11-18T08:10:23ZPairMotif: A new pattern-driven algorithm for planted (l, d) DNA motif search.1932-620310.1371/journal.pone.0048442https://doaj.org/article/f23df5d3df90474c820280cc1b2055be2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23119020/?tool=EBIhttps://doaj.org/toc/1932-6203Motif search is a fundamental problem in bioinformatics with an important application in locating transcription factor binding sites (TFBSs) in DNA sequences. The exact algorithms can report all (l, d) motifs and find the best one under a specific objective function. However, it is still a challenging task to identify weak motifs, since either a large amount of memory or execution time is required by current exact algorithms. A new exact algorithm, PairMotif, is proposed for planted (l, d) motif search (PMS) in this paper. To effectively reduce both candidate motifs and scanned l-mers, multiple pairs of l-mers with relatively large distances are selected from input sequences to restrict the search space. Comparisons with several recently proposed algorithms show that PairMotif requires less storage space and runs faster on most PMS instances. Particularly, among the algorithms compared, only PairMotif can solve the weak instance (27, 9) within 10 hours. Moreover, the performance of PairMotif is stable over the sequence length, which allows it to identify motifs in longer sequences. For the real biological data, experimental results demonstrate the validity of the proposed algorithm.Qiang YuHongwei HuoYipu ZhangHongzhi GuoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 10, p e48442 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Qiang Yu Hongwei Huo Yipu Zhang Hongzhi Guo PairMotif: A new pattern-driven algorithm for planted (l, d) DNA motif search.
description	Motif search is a fundamental problem in bioinformatics with an important application in locating transcription factor binding sites (TFBSs) in DNA sequences. The exact algorithms can report all (l, d) motifs and find the best one under a specific objective function. However, it is still a challenging task to identify weak motifs, since either a large amount of memory or execution time is required by current exact algorithms. A new exact algorithm, PairMotif, is proposed for planted (l, d) motif search (PMS) in this paper. To effectively reduce both candidate motifs and scanned l-mers, multiple pairs of l-mers with relatively large distances are selected from input sequences to restrict the search space. Comparisons with several recently proposed algorithms show that PairMotif requires less storage space and runs faster on most PMS instances. Particularly, among the algorithms compared, only PairMotif can solve the weak instance (27, 9) within 10 hours. Moreover, the performance of PairMotif is stable over the sequence length, which allows it to identify motifs in longer sequences. For the real biological data, experimental results demonstrate the validity of the proposed algorithm.
format	article
author	Qiang Yu Hongwei Huo Yipu Zhang Hongzhi Guo
author_facet	Qiang Yu Hongwei Huo Yipu Zhang Hongzhi Guo
author_sort	Qiang Yu
title	PairMotif: A new pattern-driven algorithm for planted (l, d) DNA motif search.
title_short	PairMotif: A new pattern-driven algorithm for planted (l, d) DNA motif search.
title_full	PairMotif: A new pattern-driven algorithm for planted (l, d) DNA motif search.
title_fullStr	PairMotif: A new pattern-driven algorithm for planted (l, d) DNA motif search.
title_full_unstemmed	PairMotif: A new pattern-driven algorithm for planted (l, d) DNA motif search.
title_sort	pairmotif: a new pattern-driven algorithm for planted (l, d) dna motif search.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/f23df5d3df90474c820280cc1b2055be
work_keys_str_mv	AT qiangyu pairmotifanewpatterndrivenalgorithmforplantedlddnamotifsearch AT hongweihuo pairmotifanewpatterndrivenalgorithmforplantedlddnamotifsearch AT yipuzhang pairmotifanewpatterndrivenalgorithmforplantedlddnamotifsearch AT hongzhiguo pairmotifanewpatterndrivenalgorithmforplantedlddnamotifsearch
_version_	1718422144624361472

PairMotif: A new pattern-driven algorithm for planted (l, d) DNA motif search.

Ejemplares similares