Comprehensive toolkit for generating various numerical representation schemes of DNA sequence. The descriptors included in the rDNAse package are extensively utilized in bioinformatics and chemogenomics.

• Nucleic acid composition

  • Basic kmer
  • Reverse compliment kmer
  • Increment of diversity

• Autocorrelation

  • Dinucleotide-based auto covariance
  • Dinucleotide-based cross covariance
  • Dinucleotide-based auto-cross covariance
  • Trinucleotide-based auto covariance
  • Trinucleotide-based cross covariance
  • Trinucleotide-based auto-cross covariance

• Nucleic acid composition

  • Pseudo dinucleotide composition
  • Pseudo k-tupler nucleotide composition

Local and global pairwise sequence alignment for DNA sequences:

• Between two DNA sequences
• Parallelized pairwise similarity calculation with a list of DNA sequences

GO semantic similarity measures:

• Between two groups of GO terms / two Entrez Gene IDs
• Parallelized pairwise similarity calculation with a list of GO terms / Entrez Gene IDs

• CRAN: https://cran.r-project.org/package=rDNAse
• GitHub: https://github.com/wind22zhu/rDNAse
• Bug report: https://github.com/wind22zhu/rDNAse/issues