Pseudo K-tuple nucleotide composition
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The Pseudo K-tuple nucleotide composition or PseKNC, was extended from Chou's Pseudo amino acid composition (PseAAC).[1] Both PseAAC and PseKNC are of vector descriptor, but the former represents protein or peptide sequences while the latter represents DNA or RNA sequences.
To avoid completely losing the sequence-order information for protein and peptide sequences, the PseAAC[1] was proposed by Kuo-Chen Chou. To address the problem of DNA and RNA sequences, the pseudo K-tuple nucleotide composition or PseKNC was proposed.[2][3][4] For the convenience scientific community, a freely available web server called PseKNC[2] and an open source package called PseKNC-General[3] were developed in 2013 and 2014, respectively, that could convert large-scale sequence datasets to pseudo nucleotide compositions with numerous choices of physicochemical property combinations. PseKNC-General can generate several modes of pseudo nucleotide compositions, including conventional k-tuple nucleotide compositions, Moreau–Broto autocorrelation coefficient, Moran autocorrelation coefficient, Geary autocorrelation coefficient, Type I PseKNC and Type II PseKNC.
Like PseAAC in computational proteomics and proteome analysis, PseKNC has also been increasingly used in computational genomics and performing various genome analyses.
References
edit- ^ a b Chou, Kuo-Chen (2001). "Prediction of protein cellular attributes using pseudo-amino acid composition". Proteins: Structure, Function, and Genetics. 43 (3): 246–55. doi:10.1002/prot.1035. PMID 11288174. S2CID 28406797.
- ^ a b Chen, Wei; Lei, Tian-Yu; Jin, Dian-Chuan; Lin, Hao; Chou, Kuo-Chen (2014). "PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition". Analytical Biochemistry. 456: 53–60. doi:10.1016/j.ab.2014.04.001. PMID 24732113.
- ^ a b Chen, Wei; Zhang, Xitong; Brooker, Jordan; Lin, Hao; Zhang, Liqing; Chou, Kuo-Chen (2015). "PseKNC-General: A cross-platform package for generating various modes of pseudo nucleotide compositions". Bioinformatics. 31 (1): 119–20. doi:10.1093/bioinformatics/btu602. PMID 25231908.
- ^ Chen, Wei; Lin, Hao; Chou, Kuo-Chen (2015). "Pseudo nucleotide composition or PseKNC: An effective formulation for analyzing genomic sequences". Molecular BioSystems. 11 (10): 2620–34. doi:10.1039/c5mb00155b. PMID 26099739.