iTIS-PseTNC

iTIS-PseTNC: a sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition. Translation is a key process for gene expression. Timely identification of the translation initiation site (TIS) is very important for conducting in-depth genome analysis. With the avalanche of genome sequences generated in the postgenomic age, it is highly desirable to develop automated methods for rapidly and effectively identifying TIS. Although some computational methods were proposed in this regard, none of them considered the global or long-range sequence-order effects of DNA, and hence their prediction quality was limited. To count this kind of effects, a new predictor, called ”iTIS-PseTNC,” was developed by incorporating the physicochemical properties into the pseudo trinucleotide composition, quite similar to the PseAAC (pseudo amino acid composition) approach widely used in computational proteomics. It was observed by the rigorous cross-validation test on the benchmark dataset that the overall success rate achieved by the new predictor in identifying TIS locations was over 97%. As a web server, iTIS-PseTNC is freely accessible at http://lin.uestc.edu.cn/server/iTIS-PseTNC. To maximize the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web server to obtain the desired results without the need to go through detailed mathematical equations, which are presented in this paper just for the integrity of the new prection method.


References in zbMATH (referenced in 15 articles )

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  1. 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)
  2. 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)
  3. Mei, Juan; Fu, Yi; Zhao, Ji: Analysis and prediction of ion channel inhibitors by using feature selection and Chou’s general pseudo amino acid composition (2018)
  4. Srivastava, Abhishikha; Kumar, Ravindra; Kumar, Manish: BlaPred: predicting and classifying (\beta)-lactamase using a 3-tier prediction system via Chou’s general PseAAC (2018)
  5. Saghapour, Ehsan; Sehhati, Mohammadreza: Prediction of metastasis in advanced colorectal carcinomas using CGH data (2017)
  6. Jia, Jianhua; Liu, Zi; Xiao, Xuan; Liu, Bingxiang; Chou, Kuo-Chen: pSuc-Lys: predict lysine succinylation sites in proteins with PseAAC and ensemble random forest approach (2016)
  7. Jiao, Ya-Sen; Du, Pu-Feng: Predicting Golgi-resident protein types using pseudo amino acid compositions: approaches with positional specific physicochemical properties (2016)
  8. Ali, Farman; Hayat, Maqsood: Classification of membrane protein types using voting feature interval in combination with Chou’s pseudo amino acid composition (2015)
  9. Bag, Susmita; Ramaiah, Sudha; Anbarasu, Anand: fabp4 is central to eight obesity associated genes: a functional gene network-based polymorphic study (2015)
  10. Golzari, Fahimeh; Jalili, Saeed: VR-BFDT: a variance reduction based binary fuzzy decision tree induction method for protein function prediction (2015)
  11. Ju, Zhe; Cao, Jun-Zhe; Gu, Hong: iLM-2L: a two-level predictor for identifying protein lysine methylation sites and their methylation degrees by incorporating K-gap amino acid pairs into Chou’s general PseAAC (2015)
  12. Khan, Zaheer Ullah; Hayat, Maqsood; Khan, Muazzam Ali: Discrimination of acidic and alkaline enzyme using Chou’s pseudo amino acid composition in conjunction with probabilistic neural network model (2015)
  13. Kou, Gaoshan; Feng, Yonge: Identify five kinds of simple super-secondary structures with quadratic discriminant algorithm based on the chemical shifts (2015)
  14. Kumar, Ravindra; Srivastava, Abhishikha; Kumari, Bandana; Kumar, Manish: Prediction of (\beta)-lactamase and its class by Chou’s pseudo-amino acid composition and support vector machine (2015)
  15. Li, Xiong; Liao, Bo; Chen, Haowen: A new technique for generating pathogenic barcodes in breast cancer susceptibility analysis (2015)