PseKNC-General: A cross-platform package for generating various modes of pseudo nucleotide compositions

Abstract

Summary: The avalanche of genomic sequences generated in the post-genomic age requires efficient computational methods for rapidly and accurately identifying biological features from sequence information. Towards this goal, we developed a freely available and open-source package, called PseKNC-General (the general form of pseudo k-tuple nucleotide composition), that allows for fast and accurate computation of all the widely used nucleotide structural and physicochemical properties of both DNA and RNA sequences. 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. In every mode, >100 physicochemical properties are available for choosing. Moreover, it is flexible enough to allow the users to calculate PseKNC with user-defined properties. The package can be run on Linux, Mac and Windows systems and also provides a graphical user interface. Availability and implementation: The package is freely available at: http://lin.uestc.edu.cn/server/pseknc. Contact: or lqzhang@vt.edu or kcchou@gordonlifescience.org. Supplementary information: Supplementary data are available at Bioinformatics online.