kmeRs: 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) <doi:10.1016/0022-2836(70)90057-4> global or Smith-Waterman (1981) <doi:10.1016/0022-2836(81)90087-5> 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.

Package details

AuthorRafal Urniaz [aut, cre] (<>)
Bioconductor views Software
MaintainerRafal Urniaz <[email protected]>
Package repositoryView on CRAN
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kmeRs documentation built on Nov. 3, 2018, 5:03 p.m.