K-Mers Similarity Score Matrix

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 (1970) global or Smith-Waterman (1981) local alignment. 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.


Reference manual

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1.1.0 by Rafal Urniaz, a year ago


Report a bug at http://github.com/RafalUrniaz/kmeRs/issues

Browse source code at https://github.com/cran/kmeRs

Authors: Rafal Urniaz [aut, cre]

Documentation:   PDF Manual  

GPL-3 license

Imports tcR, rDNAse, utils, stats, Biostrings

Suggests knitr, ape, rmarkdown

See at CRAN