Prediction of DNase I Hypersensitive Sites by Using Pseudo Nucleotide Compositions

Prediction of DNase I Hypersensitive Sites by Using Pseudo Nucleotide Compositions

DNase I hypersensitive sites (DHS) associated with a wide variety of regulatory DNA elements. Knowledge about the locations of DHS is helpful for deciphering the function of noncoding genomic regions. With the acceleration of genome sequences in the postgenomic age, it is highly desired to develop c...

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Main Authors: Pengmian Feng, Ning Jiang, Nan Liu
Format: Article
Language:English
Published: Hindawi Limited 2014-01-01
Series:The Scientific World Journal
Online Access:http://dx.doi.org/10.1155/2014/740506
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spelling doaj-92eb2daea8fa40bda81aea1919d8f2802020-11-24T21:50:57ZengHindawi LimitedThe Scientific World Journal2356-61401537-744X2014-01-01201410.1155/2014/740506740506Prediction of DNase I Hypersensitive Sites by Using Pseudo Nucleotide CompositionsPengmian Feng0Ning Jiang1Nan Liu2School of Public Health, Hebei United University, Tangshan 063000, ChinaSchool of Public Health, Hebei United University, Tangshan 063000, ChinaSchool of Public Health, Hebei United University, Tangshan 063000, ChinaDNase I hypersensitive sites (DHS) associated with a wide variety of regulatory DNA elements. Knowledge about the locations of DHS is helpful for deciphering the function of noncoding genomic regions. With the acceleration of genome sequences in the postgenomic age, it is highly desired to develop cost-effective computational methods to identify DHS. In the present work, a support vector machine based model was proposed to identify DHS by using the pseudo dinucleotide composition. In the jackknife test, the proposed model obtained an accuracy of 83%, which is competitive with that of the existing method. This result suggests that the proposed model may become a useful tool for DHS identifications.http://dx.doi.org/10.1155/2014/740506
collection DOAJ
language English
format Article
sources DOAJ
author Pengmian Feng
Ning Jiang
Nan Liu
spellingShingle Pengmian Feng
Ning Jiang
Nan Liu
Prediction of DNase I Hypersensitive Sites by Using Pseudo Nucleotide Compositions
The Scientific World Journal
author_facet Pengmian Feng
Ning Jiang
Nan Liu
author_sort Pengmian Feng
title Prediction of DNase I Hypersensitive Sites by Using Pseudo Nucleotide Compositions
title_short Prediction of DNase I Hypersensitive Sites by Using Pseudo Nucleotide Compositions
title_full Prediction of DNase I Hypersensitive Sites by Using Pseudo Nucleotide Compositions
title_fullStr Prediction of DNase I Hypersensitive Sites by Using Pseudo Nucleotide Compositions
title_full_unstemmed Prediction of DNase I Hypersensitive Sites by Using Pseudo Nucleotide Compositions
title_sort prediction of dnase i hypersensitive sites by using pseudo nucleotide compositions
publisher Hindawi Limited
series The Scientific World Journal
issn 2356-6140
1537-744X
publishDate 2014-01-01
description DNase I hypersensitive sites (DHS) associated with a wide variety of regulatory DNA elements. Knowledge about the locations of DHS is helpful for deciphering the function of noncoding genomic regions. With the acceleration of genome sequences in the postgenomic age, it is highly desired to develop cost-effective computational methods to identify DHS. In the present work, a support vector machine based model was proposed to identify DHS by using the pseudo dinucleotide composition. In the jackknife test, the proposed model obtained an accuracy of 83%, which is competitive with that of the existing method. This result suggests that the proposed model may become a useful tool for DHS identifications.
url http://dx.doi.org/10.1155/2014/740506
work_keys_str_mv AT pengmianfeng predictionofdnaseihypersensitivesitesbyusingpseudonucleotidecompositions
AT ningjiang predictionofdnaseihypersensitivesitesbyusingpseudonucleotidecompositions
AT nanliu predictionofdnaseihypersensitivesitesbyusingpseudonucleotidecompositions
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