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

Build Status GPLv3 license CRAN_Status_Badge Codacy Badge

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

TBA

Installation

Biostrings needs to be installed first,

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Biostrings")

then:

# Install from CRAN
install.packages("kmeRs")

# Or the development version from GitHub:
# install.packages("devtools")
devtools::install_github("rafalurniaz/kmeRs/kmeRs/")

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

kmeRs::kmeRs_test_package()

## Dependences

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

References

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.