protHMM
Protein Feature Extraction from Profile Hidden Markov Models
Last update: 5 July 2023
Software version identifier: 0.1.1
Copyright license: GNU General Public License
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>.
- HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
- Accelerated Profile HMM Searches
- An Ensemble Classifier with Random Projection for Predicting Protein–Protein Interactions Using Sequence and Evolutionary Information
- Protein Subcellular Localization Based on Evolutionary Information and Segmented Distribution
- Advancing the Accuracy of Protein Fold Recognition by Utilizing Profiles From Hidden Markov Models
- Probabilistic expression of spatially varied amino acid dimers into general form of Chou׳s pseudo amino acid composition for protein fold recognition
