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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Bibliographic Details
Published in:TheScientificWorld 2014-01, Vol.2014 (2014), p.1-4
Main Authors: Feng, Peng-Mian, Liu, Nan, Jiang, Ning
Format: Article
Language:English
Subjects:
Algorithms
Binding Sites
Cell Line
Chromatin - genetics
Chromatin - metabolism
Computational Biology - methods
Datasets as Topic
Deoxyribonuclease I - metabolism
Deoxyribonucleic acid
DNA
DNA - chemistry
DNA - genetics
DNA - metabolism
DNA damage
DNA sequencing
Genetic testing
Genomes
Genomics
Humans
Machine learning
Methods
Nucleotide sequencing
Single nucleotide polymorphisms
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Description
Summary: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.
ISSN:2356-6140
1537-744X
1537-744X
DOI:10.1155/2014/740506