Pse-in-One

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences. With the avalanche of biological sequences generated in the post-genomic age, one of the most challenging problems in computational biology is how to effectively formulate the sequence of a biological sample (such as DNA, RNA or protein) with a discrete model or a vector that can effectively reflect its sequence pattern information or capture its key features concerned. Although several web servers and stand-alone tools were developed to address this problem, all these tools, however, can only handle one type of samples. Furthermore, the number of their built-in properties is limited, and hence it is often difficult for users to formulate the biological sequences according to their desired features or properties. In this article, with a much larger number of built-in properties, we are to propose a much more flexible web server called Pse-in-One (http://bioinformatics.hitsz.edu.cn/Pse-in-One/), which can, through its 28 different modes, generate nearly all the possible feature vectors for DNA, RNA and protein sequences. Particularly, it can also generate those feature vectors with the properties defined by users themselves. These feature vectors can be easily combined with machine-learning algorithms to develop computational predictors and analysis methods for various tasks in bioinformatics and system biology. It is anticipated that the Pse-in-One web server will become a very useful tool in computational proteomics, genomics, as well as biological sequence analysis. Moreover, to maximize users’ convenience, its stand-alone version can also be downloaded from http://bioinformatics.hitsz.edu.cn/Pse-in-One/download/, and directly run on Windows, Linux, Unix and Mac OS.


References in zbMATH (referenced in 41 articles )

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  1. Adilina, Sheikh; Farid, Dewan Md; Shatabda, Swakkhar: Effective DNA binding protein prediction by using key features via Chou’s general PseAAC (2019)
  2. Ahmad, Jamal; Hayat, Maqsood: MFSC: multi-voting based feature selection for classification of Golgi proteins by adopting the general form of Chou’s PseAAC components (2019)
  3. Bai, Xiaolu; Chen, Xiaolin: Rational design, conformational analysis and membrane-penetrating dynamics study of Bac2A-derived antimicrobial peptides against gram-positive clinical strains isolated from pyemia (2019)
  4. Chen, Guodong; Cao, Man; Yu, Jialin; Guo, Xinyun; Shi, Shaoping: Prediction and functional analysis of prokaryote lysine acetylation site by incorporating six types of features into Chou’s general PseAAC (2019)
  5. Hussain, Waqar; Khan, Yaser Daanial; Rasool, Nouman; Khan, Sher Afzal; Chou, Kuo-Chen: SPrenylC-PseAAC: a sequence-based model developed via Chou’s 5-steps rule and general PseAAC for identifying S-prenylation sites in proteins (2019)
  6. Jia, Jianhua; Li, Xiaoyan; Qiu, Wangren; Xiao, Xuan; Chou, Kuo-Chen: iPPI-PseAAC(CGR): identify protein-protein interactions by incorporating chaos game representation into PseAAC (2019)
  7. Khan, Yaser Daanial; Jamil, Mehreen; Hussain, Waqar; Rasool, Nouman; Khan, Sher Afzal; Chou, Kuo-Chen: pSSbond-PseAAC: prediction of disulfide bonding sites by integration of PseAAC and statistical moments (2019)
  8. Ning, Qiao; Ma, Zhiqiang; Zhao, Xiaowei: Dforml(KNN)-PseAAC: detecting formylation sites from protein sequences using K-nearest neighbor algorithm via Chou’s 5-step rule and pseudo components (2019)
  9. Pan, Yi; Wang, Shiyuan; Zhang, Qi; Lu, Qianzi; Su, Dongqing; Zuo, Yongchun; Yang, Lei: Analysis and prediction of animal toxins by various Chou’s pseudo components and reduced amino acid compositions (2019)
  10. Qing, Yang; Cangzhi, Jia; Taoying, Li: Prediction of aptamer-protein interacting pairs based on sparse autoencoder feature extraction and an ensemble classifier (2019)
  11. Tahir, Muhammad; Tayara, Hilal; Chong, Kil To: iRNA-PseKNC(2methyl): identify RNA 2’-O-methylation sites by convolution neural network and Chou’s pseudo components (2019)
  12. Tian, Baoguang; Wu, Xue; Chen, Cheng; Qiu, Wenying; Ma, Qin; Yu, Bin: Predicting protein-protein interactions by fusing various Chou’s pseudo components and using wavelet denoising approach (2019)
  13. Wang, Lidong; Zhang, Ruijun; Mu, Yashuang: Fu-SulfPred: identification of protein S-sulfenylation sites by fusing forests via Chou’s general PseAAC (2019)
  14. Zhao, Wei; Li, Guang-Ping; Wang, Jun; Zhou, Yuan-Ke; Gao, Yang; Du, Pu-Feng: Predicting protein sub-Golgi locations by combining functional domain enrichment scores with pseudo-amino acid compositions (2019)
  15. Akbar, Shahid; Hayat, Maqsood: iMethyl-STTNC: identification of N(^6)-methyladenosine sites by extending the idea of SAAC into Chou’s PseAAC to formulate RNA sequences (2018)
  16. Arif, Muhammad; Hayat, Maqsood; Jan, Zahoor: IMem-2LSAAC: a two-level model for discrimination of membrane proteins and their types by extending the notion of SAAC into Chou’s pseudo amino acid composition (2018)
  17. Contreras-Torres, Ernesto: Predicting structural classes of proteins by incorporating their global and local physicochemical and conformational properties into general Chou’s PseAAC (2018)
  18. Jia, Cangzhi; Yang, Qing; Zou, Quan: NucPosPred: predicting species-specific genomic nucleosome positioning via four different modes of general PseKNC (2018)
  19. Ju, Zhe; Wang, Shi-Yun: Prediction of S-sulfenylation sites using mRMR feature selection and fuzzy support vector machine algorithm (2018)
  20. Liang, Yunyun; Zhang, Shengli: Identify Gram-negative bacterial secreted protein types by incorporating different modes of PSSM into Chou’s general PseAAC via Kullback-Leibler divergence (2018)

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