The package contains tools to calculate similarity score matrix for DNA k-mers

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kmeRs: K-Mers Similarity Score Matrix

The package contains tools to calculate similarity score matrix for DNA k-mers. The pairwise similarity score is calculated using PAM or BLOSUM substitution matrix. The results are evaluated by similarity score calculated by Needleman-Wunsch (global) (Needleman and Wunsch 1970) or Smith-Waterman (local) alignment. (Smith and Waterman 1981). Higher similarity score indicates more similar sequences for BLOSUM and less similar sequences for PAM matrix; 30, 40, 70, 120, 250 and 62, 45, 50, 62, 80, 100 matrix versions are available for PAM and BLOSUM, respectively.

How to cite



Biostrings needs to be installed first,

if (!requireNamespace("BiocManager", quietly = TRUE))



# Install from CRAN

# Or the development version from GitHub:
# install.packages("devtools")

Documentation and tutorials

The documentation like manual or tutorials can be found in documentation folder to this repository or directly from installed package by commands:

# To show the introduction vignette
vignette("Introduction_to_kmeRs_package", package="kmeRs")

# To show the manual and functions examples
help(package = "kmeRs")

Quick demo


## Dependences

Depends: R (>= 3.4.0)
Imports: tcR, rDNAse, utils, stats, Biostrings
Encoding: UTF-8


Needleman, Saul B., and Christian D. Wunsch. 1970. “A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins.” Journal of Molecular Biology 48 (3): 443–53. doi:https://doi.org/10.1016/0022-2836(70)90057-4.
Smith, T.F., and M.S. Waterman. 1981. “Identification of Common Molecular Subsequences.” Journal of Molecular Biology 147 (1): 195–97. doi:https://doi.org/10.1016/0022-2836(81)90087-5.