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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.
Getting started
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Package details |
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| Author | Rafal Urniaz [aut, cre] (<https://orcid.org/0000-0003-0192-2165>) |
| Bioconductor views | Software |
| Maintainer | Rafal Urniaz <rafal.urniaz@gmail.com> |
| License | GPL-3 |
| Version | 1.1.0 |
| URL | https://rafalurniaz.github.io/kmeRs/ |
| Package repository | View on CRAN |
| Installation |
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