msktuple: An integrated R library for alignment-free multiple sequence k-tuple analysis

作者：Amiri Saeid^*; Dinov Ivo D

来源：Chemometrics and Intelligent Laboratory Systems, 2017, 168: 84-88.

DOI：10.1016/j.chemolab.2017.07.012

• Clustering
• Dissimilarity
• Ensembling methods
• Multiple alignment-free
• k-tuple

Recently alignment-free sequence comparison methods based on promoter-frequency distance measures have gained popularity. This paper reports on the implementation and validation of several alignment-free sequence analysis methods for representing and quantifying between-sequence distances and sequence variability. The msktuple library includes the following sequence comparison techniques: locational k-tuple, naive k-tuple, CV Tree, and their ensemble variants. These metrics are used to determine the dissimilarity between sequences using k-letter words. In support of open-science, we provide open-source software, R-scripts, and protocols implementing the new techniques. These tools will support collaboration, enable independent validation, promote result reproducibility and enable tool interoperability.

• 出版日期2017-9-15