IM_psehmm

The first twenty numbers of this feature correspond to the means of each column of the HMM matrix
\(H\). The rest of the features in the feature vector are found in matrix \(T[i,j]\), where \(T[i,j] =
\frac{1}{L-i}\sum_{n = 1}^{20-i} [H_{m,n}-H_{m, n+i}]^2, m = 1:L,\space i = 1:d\space and\space j = 1:20\).

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>.

Shayaan Emran

protHMM

Protein Feature Extraction from Profile Hidden Markov Models

IM_psehmm function

<dl><dt>hmm</dt>
<dd>The name of a profile hidden markov model file.</dd>
<dt>d</dt>
<dd>The maximum distance between residues column-wise.</dd></dl>

Arguments

IM_psehmm — IM_psehmm

<dl>

<dt>hmm</dt>
<dd>The name of a profile hidden markov model file.</dd>


<dt>d</dt>
<dd>The maximum distance between residues column-wise.</dd>

</dl>

IM_psehmm: IM_psehmm

Description

Usage

Value

Arguments

References

Examples