hmm_Single_Average

This feature groups together rows that are related to the same amino acid. This is done using a vector
\(SA(k)\), in which \(k\) spans \(1:400\) and \(SA(k) = avg_{i = 1, 2... L}H[i, j] \times \delta(P(i), A(z))\),
in which \(H\) is the HMM matrix, \(P\) in the protein sequence, \(A\) is an ordered set of amino acids,
 the variables \(j, z = 1:20\), the variable \(k = j + 20 \times (z-1)\) when creating the vector,
and \(\delta()\) represents Kronecker's delta.

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

hmm_Single_Average function

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

Arguments

hmm_Single_Average — hmm_Single_Average

<dl>

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

</dl>

hmm_Single_Average: hmm_Single_Average

Description

Usage

Value

Arguments

References

Examples