protHMM: Protein Feature Extraction from Profile Hidden Markov Models

Calculates a comprehensive list of features from profile hidden Markov models (HMMs) of proteins. Adapts and ports features for use with HMMs instead of Position Specific Scoring Matrices, in order to take advantage of more accurate multiple sequence alignment by programs such as 'HHBlits' Remmert et al. (2012) <doi:10.1038/nmeth.1818> and 'HMMer' Eddy (2011) <doi:10.1371/journal.pcbi.1002195>. Features calculated by this package can be used for protein fold classification, protein structural class prediction, sub-cellular localization and protein-protein interaction, among other tasks. Some examples of features extracted are found in Song et al. (2018) <doi:10.3390/app8010089>, Jin & Zhu (2021) <doi:10.1155/2021/8629776>, Lyons et al. (2015) <doi:10.1109/tnb.2015.2457906> and Saini et al. (2015) <doi:10.1016/j.jtbi.2015.05.030>.

Version: 0.1.1
Imports: gtools, utils, stats, phonTools
Suggests: covr, knitr, rmarkdown, testthat (≥ 3.0.0)
Published: 2023-07-05
DOI: 10.32614/CRAN.package.protHMM
Author: Shayaan Emran [aut, cre, cph]
Maintainer: Shayaan Emran <shayaan.emran at>
License: GPL (≥ 3)
NeedsCompilation: no
Materials: README NEWS
CRAN checks: protHMM results


Reference manual: protHMM.pdf
Vignettes: protHMM


Package source: protHMM_0.1.1.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): protHMM_0.1.1.tgz, r-oldrel (arm64): protHMM_0.1.1.tgz, r-release (x86_64): protHMM_0.1.1.tgz, r-oldrel (x86_64): protHMM_0.1.1.tgz


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