iNuc-PhysChem: A Sequence-Based Predictor for Identifying Nucleosomes via Physicochemical Properties
Open Access
- 29 October 2012
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 7 (10), e47843
- https://doi.org/10.1371/journal.pone.0047843
Abstract
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.Keywords
This publication has 80 references indexed in Scilit:
- Positional variations among heterogeneous nucleosome maps give dynamical information on chromatinChromosoma, 2010
- Nucleosome positioning by genomic excluding-energy barriersProceedings of the National Academy of Sciences of the United States of America, 2009
- Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivoNature Structural & Molecular Biology, 2009
- DNA physical properties determine nucleosome occupancy from yeast to flyNucleic Acids Research, 2008
- A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioningGenome Research, 2008
- Dynamic Regulation of Nucleosome Positioning in the Human GenomeCell, 2008
- A high-resolution atlas of nucleosome occupancy in yeastNature Genetics, 2007
- Sequence-dependent DNA deformability studied using molecular dynamics simulationsNucleic Acids Research, 2007
- A genomic code for nucleosome positioningNature, 2006
- Prediction of protein cellular attributes using pseudo‐amino acid compositionProteins-Structure Function and Bioinformatics, 2001