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Predicting Gram-positive bacterial protein subcellular localization based on localization motifs

Hu, Yinxia ; Li, Tonghua ; Sun, Jiangming LU orcid ; Tang, Shengnan ; Xiong, Wenwei ; Li, Dapeng ; Chen, Guanyan and Cong, Peisheng (2012) In Journal of Theoretical Biology 308. p.135-140
Abstract

The subcellular localization of proteins is closely related to their functions. In this work, we propose a novel approach based on localization motifs to improve the accuracy of predicting subcellular localization of Gram-positive bacterial proteins. Our approach performed well on a five-fold cross validation with an overall success rate of 89.5%. Besides, the overall success rate of an independent testing dataset was 97.7%. Moreover, our approach was tested using a new experimentally-determined set of Gram-positive bacteria proteins and achieved an overall success rate of 96.3%.

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author
; ; ; ; ; ; and
publishing date
type
Contribution to journal
publication status
published
keywords
Motif finding, Position-specific frequencies encoding, Subcellular location prediction, Support vector machine (SVM)
in
Journal of Theoretical Biology
volume
308
pages
135 - 140
publisher
Academic Press
external identifiers
  • scopus:84862677130
  • pmid:22683368
ISSN
0022-5193
DOI
10.1016/j.jtbi.2012.05.031
language
English
LU publication?
no
additional info
Funding Information: The authors would like to thank financial support by the National Natural Science Foundation of China ( 20675057 , 20705024 ).
id
8238ff44-b063-431c-9a8d-685a0034ebf8
date added to LUP
2023-05-03 22:05:55
date last changed
2024-03-08 00:34:32
@article{8238ff44-b063-431c-9a8d-685a0034ebf8,
  abstract     = {{<p>The subcellular localization of proteins is closely related to their functions. In this work, we propose a novel approach based on localization motifs to improve the accuracy of predicting subcellular localization of Gram-positive bacterial proteins. Our approach performed well on a five-fold cross validation with an overall success rate of 89.5%. Besides, the overall success rate of an independent testing dataset was 97.7%. Moreover, our approach was tested using a new experimentally-determined set of Gram-positive bacteria proteins and achieved an overall success rate of 96.3%.</p>}},
  author       = {{Hu, Yinxia and Li, Tonghua and Sun, Jiangming and Tang, Shengnan and Xiong, Wenwei and Li, Dapeng and Chen, Guanyan and Cong, Peisheng}},
  issn         = {{0022-5193}},
  keywords     = {{Motif finding; Position-specific frequencies encoding; Subcellular location prediction; Support vector machine (SVM)}},
  language     = {{eng}},
  month        = {{09}},
  pages        = {{135--140}},
  publisher    = {{Academic Press}},
  series       = {{Journal of Theoretical Biology}},
  title        = {{Predicting Gram-positive bacterial protein subcellular localization based on localization motifs}},
  url          = {{http://dx.doi.org/10.1016/j.jtbi.2012.05.031}},
  doi          = {{10.1016/j.jtbi.2012.05.031}},
  volume       = {{308}},
  year         = {{2012}},
}