Psortb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Motivation: PSORTb v.1.1 is the most precise bacterial localization prediction tool available. However, the program’s predictive coverage and recall are low and the method is only applicable to Gram-negative bacteria. The goals of the present work are as follows: increase PSORTb’s coverage while maintaining the existing precision level, expand it to include Gram-positive bacteria and then carry out a comparative analysis of localization. Results: An expanded database of proteins of known localization and new modules using frequent subsequence-based support vector machines was introduced into PSORTb v.2.0. The program attains a precision of 96% for Gram-positive and Gram-negative bacteria and predictive coverage comparable to other tools for whole proteome analysis. We show that the proportion of proteins at each localization is remarkably consistent across species, even in species with varying proteome size. Availability: Web-based version: Standalone version: Available through the website under GNU General Public License.

References in zbMATH (referenced in 18 articles )

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  1. Cheng, Xiang; Xiao, Xuan; Chou, Kuo-Chen: pLoc_bal-mGneg: predict subcellular localization of Gram-negative bacterial proteins by quasi-balancing training dataset and general PseAAC (2018)
  2. Stritzler, Margarita; Berini, Carolina; Jozefkowicz, Cintia; Soto, Gabriela; Ayub, Nicolás: Understanding the intracellular-to-extracellular localization switch of polyhydroxybutyrate polymerase in \textitPseudomonasbackgrounds as a microevolutionary process (2018)
  3. Arango-Argoty, G. A.; Jaramillo-Garzón, J. A.; Castellanos-Domínguez, G.: Feature extraction by statistical contact potentials and wavelet transform for predicting subcellular localizations in gram negative bacterial proteins (2015)
  4. Zhu, Chengzhang; Liu, Xinwang; Liu, Qiang; Ming, Yuewei; Yin, Jianping: Distance based multiple kernel ELM: a fast multiple kernel learning approach (2015)
  5. Wang, Han; Liu, Bo; Sun, Pingping; Ma, Zhiqiang: A topology structure based outer membrane proteins segment alignment method (2013) ioport
  6. Hu, Yinxia; Li, Tonghua; Sun, Jiangming; Tang, Shengnan; Xiong, Wenwei; Li, Dapeng; Chen, Guanyan; Cong, Peisheng: Predicting Gram-positive bacterial protein subcellular localization based on localization motifs (2012)
  7. Xiao, Xuan; Wu, Zhi-Cheng; Chou, Kuo-Chen: \textbfiLoc-Virus: a multi-label learning classifier for identifying the subcellular localization of virus proteins with both single and multiple sites (2011)
  8. Zakeri, Pooya; Moshiri, Behzad; Sadeghi, Mehdi: Prediction of protein submitochondria locations based on data fusion of various features of sequences (2011)
  9. Shen, Hong-Bin; Chou, Kuo-Chen: Gneg-mPLoc: a top-down strategy to enhance the quality of predicting subcellular localization of Gram-negative bacterial proteins (2010)
  10. Yu, Lezheng; Guo, Yanzhi; Li, Yizhou; Li, Gongbing; Li, Menglong; Luo, Jiesi; Xiong, Wenjia; Qin, Wenli: SecretP: identifying bacterial secreted proteins by fusing new features into Chou’s pseudo-amino acid composition (2010)
  11. Arakawa, Kazuharu; Tamaki, Satoshi; Kono, Nobuaki; Kido, Nobuhiro; Ikegami, Keita; Ogawa, Ryu; Tomita, Masaru: Genome projector: zoomable genome map with multiple views (2009) ioport
  12. Xu, Qian; Hu, Derek Hao; Xue, Hong; Yu, Weichuan; Yang, Qiang: Semi-supervised protein subcellular localization (2009) ioport
  13. Baralis, Elena; Chiusano, Silvia; Dutto, Riccardo: Applying sequential rules to protein localization prediction (2008)
  14. Hu, Jing; Yan, Changhui: A method for discovering transmembrane beta-barrel proteins in Gram-negative bacterial proteomes (2008)
  15. Lin, Hao: The modified Mahalanobis discriminant for predicting outer membrane proteins by using Chou’s pseudo amino acid composition (2008)
  16. Yan, Changhui; Hu, Jing; Wang, Yingfeng: Discrimination of outer membrane proteins with improved performance (2008) ioport
  17. Gromiha, M. Michael; Ahmad, Shandar; Suwa, Makiko: Application of residue distribution along the sequence for discriminating outer membrane proteins (2005)
  18. Gardy, Jennifer L.; Spencer, Cory; Wang, Ke; Ester, Martin; Tusnády, Gábor E.; Simon, István; Hua, Sujun; De Fays, Katalin; Lambert, Christophe G.; Nakai, Kenta; Brinkman, Fiona S. L.: PSORT-B: Improving protein subcellular localization prediction for gram-negative bacteria. (2003) ioport