Natural vs. random protein sequences: discovering combinatorics properties on amino acid words

DOI10.1016/J.JTBI.2015.11.022zbMATHOpenAlexWikidataMaRDI QIDQ304845FDO

Authors Daniele Santoni, Giovanni Felici, Davide Vergni

Publication date 26 August 2016

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jtbi.2015.11.022

zbMATH Keywords

amino acid associationcombinatorics of wordsprotein sequencerandom sequence

Mathematics Subject Classification ID

Permutations, words, matrices (05A05) Protein sequences, DNA sequences (92D20)

Recommendations

• Mathematical models of random arrangements of amino acids in sequences
• The pattern recognition of probability distributions of amino acids in protein families
• Nonlinear deterministic structures and the randomness of protein sequences.
• Invitation to protein sequence analysis through probability and information
• Algorithmic complexity of protein identification: Combinatorics of weighted strings
• On the syntactic structure of protein sequences and the concept of grammar complexity
• Towards a Dynamical Systems Approach to Protein Sequence Structure
• On the computational complexity of designing DNA randomizations in a combinatorial protein experiment

Cites work

• Improvements to Platt's SMO Algorithm for SVM Classifier Design
• Learning the kernel matrix with semidefinite programming
• Natural/random protein classification models based on star network topological indices
• Support-vector networks
• Topological maps of protein sequences

Cited in

(9)

• RUNS OF AMINO ACIDS ARE LONGER THAN EXPECTED IN PROTEINS BASED ON A GRAPH THEORY REPRESENTATION OF THE GENETIC CODE
• Nonlinear deterministic structures and the randomness of protein sequences.
• Natural/random protein classification models based on star network topological indices
• Walking through protein sequence space
• Mathematical models of random arrangements of amino acids in sequences
• Characterization of protein primary sequences based on partial ordering
• Co-evolution and information signals in biological sequences
• Elman RNN based classification of proteins sequences on account of their mutual information
• Co-evolution and Information Signals in Biological Sequences

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