iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties.

Nucleosome positioning has important roles in key cellular processes. Although intensive efforts have been made in this area, the rules defining nucleosome positioning is still elusive and debated. In this study, we carried out a systematic comparison among the profiles of twelve DNA physicochemical...

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Autores principales:	Wei Chen, Hao Lin, Peng-Mian Feng, Chen Ding, Yong-Chun Zuo, Kuo-Chen Chou
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d092bfa943e44dee9391383688a4e6b8
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spelling	oai:doaj.org-article:d092bfa943e44dee9391383688a4e6b82021-11-18T08:10:47ZiNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties.1932-620310.1371/journal.pone.0047843https://doaj.org/article/d092bfa943e44dee9391383688a4e6b82012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23144709/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Nucleosome positioning has important roles in key cellular processes. Although intensive efforts have been made in this area, the rules defining nucleosome positioning is still elusive and debated. In this study, we carried out a systematic comparison among the profiles of twelve DNA physicochemical features between the nucleosomal and linker sequences in the Saccharomyces cerevisiae genome. We found that nucleosomal sequences have some position-specific physicochemical features, which can be used for in-depth studying nucleosomes. Meanwhile, a new predictor, called iNuc-PhysChem, was developed for identification of nucleosomal sequences by incorporating these physicochemical properties into a 1788-D (dimensional) feature vector, which was further reduced to a 884-D vector via the IFS (incremental feature selection) procedure to optimize the feature set. It was observed by a cross-validation test on a benchmark dataset that the overall success rate achieved by iNuc-PhysChem was over 96% in identifying nucleosomal or linker sequences. As a web-server, iNuc-PhysChem is freely accessible to the public at http://lin.uestc.edu.cn/server/iNuc-PhysChem. For the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics that were presented just for the integrity in developing the predictor. Meanwhile, for those who prefer to run predictions in their own computers, the predictor's code can be easily downloaded from the web-server. It is anticipated that iNuc-PhysChem may become a useful high throughput tool for both basic research and drug design.Wei ChenHao LinPeng-Mian FengChen DingYong-Chun ZuoKuo-Chen ChouPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 10, p e47843 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Wei Chen Hao Lin Peng-Mian Feng Chen Ding Yong-Chun Zuo Kuo-Chen Chou iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties.
description	Nucleosome positioning has important roles in key cellular processes. Although intensive efforts have been made in this area, the rules defining nucleosome positioning is still elusive and debated. In this study, we carried out a systematic comparison among the profiles of twelve DNA physicochemical features between the nucleosomal and linker sequences in the Saccharomyces cerevisiae genome. We found that nucleosomal sequences have some position-specific physicochemical features, which can be used for in-depth studying nucleosomes. Meanwhile, a new predictor, called iNuc-PhysChem, was developed for identification of nucleosomal sequences by incorporating these physicochemical properties into a 1788-D (dimensional) feature vector, which was further reduced to a 884-D vector via the IFS (incremental feature selection) procedure to optimize the feature set. It was observed by a cross-validation test on a benchmark dataset that the overall success rate achieved by iNuc-PhysChem was over 96% in identifying nucleosomal or linker sequences. As a web-server, iNuc-PhysChem is freely accessible to the public at http://lin.uestc.edu.cn/server/iNuc-PhysChem. For the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics that were presented just for the integrity in developing the predictor. Meanwhile, for those who prefer to run predictions in their own computers, the predictor's code can be easily downloaded from the web-server. It is anticipated that iNuc-PhysChem may become a useful high throughput tool for both basic research and drug design.
format	article
author	Wei Chen Hao Lin Peng-Mian Feng Chen Ding Yong-Chun Zuo Kuo-Chen Chou
author_facet	Wei Chen Hao Lin Peng-Mian Feng Chen Ding Yong-Chun Zuo Kuo-Chen Chou
author_sort	Wei Chen
title	iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties.
title_short	iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties.
title_full	iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties.
title_fullStr	iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties.
title_full_unstemmed	iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties.
title_sort	inuc-physchem: a sequence-based predictor for identifying nucleosomes via physicochemical properties.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/d092bfa943e44dee9391383688a4e6b8
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iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties.

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