hmm_SCSH

This feature returns the 2 and 3-mer compositions of the protein sequence. This is done by first
finding all possible 2 and 3-mers for any protein (\(20^2\) and \(20^3\) permutations for 2 and 3-mers respectively).
With those permutations, vectors of length 400 and 8000 are created, each point corresponding to one 2 or 3-mer.
Then, the protein sequence that corresponds to the HMM scores is extracted, and put into a bipartite graph with the protein sequence.
Each possible path of length 1 or 2 is found, and the corresponding vertices on the graph are noted as 2 and 3-mers.
For each 2 or 3-mer found from these paths, 1 is added to the position that responds to that 2/3-mer in the
2-mer and 3-mer vectors , which are the length 400 and 8000 vectors created previously. The vectors are then returned.

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_SCSH function

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

Arguments

hmm_SCSH — hmm_SCSH

<dl>

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

</dl>

hmm_SCSH: hmm_SCSH

Description

Usage

Value

Arguments

References

Examples