PseKNC

PseKNC: a flexible web server for generating pseudo K-tuple nucleotide composition. The pseudo oligonucleotide composition, or pseudo K-tuple nucleotide composition (PseKNC), can be used to represent a DNA or RNA sequence with a discrete model or vector yet still keep considerable sequence order information, particularly the global or long-range sequence order information, via the physicochemical properties of its constituent oligonucleotides. Therefore, the PseKNC approach may hold very high potential for enhancing the power in dealing with many problems in computational genomics and genome sequence analysis. However, dealing with different DNA or RNA problems may need different kinds of PseKNC. Here, we present a flexible and user-friendly web server for PseKNC (at http://lin.uestc.edu.cn/pseknc/default.aspx) by which users can easily generate many different modes of PseKNC according to their need by selecting various parameters and physicochemical properties. Furthermore, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the current web server to generate their desired PseKNC without the need to follow the complicated mathematical equations, which are presented in this article just for the integrity of PseKNC formulation and its development. It is anticipated that the PseKNC web server will become a very useful tool in computational genomics and genome sequence analysis.


References in zbMATH (referenced in 31 articles )

Showing results 21 to 31 of 31.
Sorted by year (citations)
  1. 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)
  2. Jiao, Ya-Sen; Du, Pu-Feng: Prediction of Golgi-resident protein types using general form of Chou’s pseudo-amino acid compositions: approaches with minimal redundancy maximal relevance feature selection (2016)
  3. Jiao, Ya-Sen; Du, Pu-Feng: Predicting Golgi-resident protein types using pseudo amino acid compositions: approaches with positional specific physicochemical properties (2016)
  4. Zhang, Qiang; Li, Hong; Zhao, Xiaoqing; Zheng, Yan; Meng, Hu; Jia, Yun; Xue, Hui; Bo, Sulin: Analysis on the preference for sequence matching between mRNA sequences and the corresponding introns in ribosomal protein genes (2016)
  5. Ali, Farman; Hayat, Maqsood: Classification of membrane protein types using voting feature interval in combination with Chou’s pseudo amino acid composition (2015)
  6. Bag, Susmita; Ramaiah, Sudha; Anbarasu, Anand: fabp4 is central to eight obesity associated genes: a functional gene network-based polymorphic study (2015)
  7. Ding, Yanrui; Wang, Xueqin; Mou, Zhaolin: Communities in the iron superoxide dismutase amino acid network (2015)
  8. 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)
  9. 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)
  10. Liu, Guoqing; Xing, Yongqiang; Cai, Lu: Using weighted features to predict recombination hotspots in \textitSaccharomycescerevisiae (2015)
  11. Zhang, Qiang; Li, Hong; Zhao, Xiaoqing; Zheng, Yan; Zhou, Deliang: Distribution bias of the sequence matching between exons and introns in exon joint and EJC binding region in \textitC. elegans (2015)