rDNAse
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.
Package Description
Commonly used descriptors
-
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
Similarity Computation
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