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protHMM  

Protein Feature Extraction from Profile Hidden Markov Models
View on CRAN: Click here


Download and install protHMM package within the R console
Install from CRAN:
install.packages("protHMM")

Install from Github:
library("remotes")
install_github("cran/protHMM")

Install by package version:
library("remotes")
install_version("protHMM", "0.1.1")



Attach the package and use:
library("protHMM")
Maintained by
Shayaan Emran
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2023-07-05
Latest Update: 2023-07-05
Description:
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) and 'HMMer' Eddy (2011) . 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) , Jin & Zhu (2021) , Lyons et al. (2015) and Saini et al. (2015) .
How to cite:
Shayaan Emran (2023). protHMM: Protein Feature Extraction from Profile Hidden Markov Models. R package version 0.1.1, https://cran.r-project.org/web/packages/protHMM. Accessed 05 Mar. 2026.
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Complete documentation for protHMM
Functions, R codes and Examples using the protHMM R package
Some associated functions: IM_psehmm . chmm . fp_hmm . hmm_GA . hmm_GSD . hmm_LBP . hmm_LPC . hmm_MA . hmm_MB . hmm_SCSH . hmm_SepDim . hmm_Single_Average . hmm_ac . hmm_bigrams . hmm_cc . hmm_distance . hmm_read . hmm_smooth . hmm_svd . hmm_trigrams . pse_hmm . 
Some associated R codes: AC.R . Bigrams.R . CC.R . CHMM.R . Distance.R . FP_HMM.R . GSD.R . Geary.R . IM_PSEHMM.R . LBP.R . LPC.R . Moran.R . MoreauBroto.R . PSE_HMM.R . Read.R . SCSH.R . SVD.R . SepDimers.R . SingleAverage.R . Smooth.R . Trigrams.R .  Full protHMM package functions and examples
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