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Related Concept Videos

Per-Unit Sequence Models01:26

Per-Unit Sequence Models

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An ideal Y-Y transformer, grounded through neutral impedances, displays per-unit sequence networks akin to those of a single-phase ideal transformer when subjected to balanced positive- or negative-sequence currents. These currents do not produce neutral currents, and their associated voltage drops.
Zero-sequence currents, which are identical in magnitude and phase, generate a neutral current, resulting in voltage drops across the neutral impedance and the low-voltage winding. If the...
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Conservation of Protein Domains Over Different Proteins02:26

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Sequence Networks of Rotating Machines01:24

Sequence Networks of Rotating Machines

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A Y-connected synchronous generator, grounded through a neutral impedance, is designed to produce balanced internal phase voltages with only positive-sequence components. The generator's sequence networks include a source voltage that is exclusively in the positive-sequence network. The sequence components of line-to-ground voltages at the generator terminals illustrate this configuration.
Zero-sequence current induces a voltage drop across the generator's neutral impedance and other...
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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Protein Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Protein sequence comparison based on representation on a finite dimensional unit hypercube.

Soumen Ghosh1,2, Jayanta Pal3, Carlo Cattani4

  • 1Electronics & Communication Engineering, National Institute of Technology, Durgapur, West Bengal, India.

Journal of Biomolecular Structure & Dynamics
|October 14, 2023
PubMed
Summary
This summary is machine-generated.

This study introduces a novel method for protein sequence comparison using physicochemical properties, generating accurate phylogenetic trees. The approach demonstrates superior efficiency and rational perception compared to existing methods.

Keywords:
ClustalWSingle property descriptor (SPD)generalized NTV metricphysiochemical propertyrank correlation coefficientrationalized perceptionsymmetric distance

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Computational Biology

Background:

  • Protein sequence comparison is crucial for understanding biological function and evolution.
  • Existing methods often rely on complex algorithms and may lack efficiency.
  • Physicochemical properties of amino acids offer a valuable, yet underexplored, basis for sequence analysis.

Purpose of the Study:

  • To develop a novel, efficient method for protein sequence comparison and phylogenetic tree construction.
  • To represent protein sequences using single physicochemical property values in a high-dimensional space.
  • To evaluate the accuracy and efficiency of the proposed method against established techniques.

Main Methods:

  • Representing protein sequences as vectors based on single physicochemical property values (e.g., polarity, molecular weight).
  • Utilizing a generalized NTV metric for calculating distance matrices between protein sequences.
  • Constructing phylogenetic trees using the neighbor-joining method in MEGA11 software.
  • Applying the method to diverse datasets including mitochondrial proteins, transcription factors, viruses, and protein kinase C family members.

Main Results:

  • Phylogenetic trees derived from different single property values (polarity, molecular weight) were identical, indicating robustness.
  • The proposed method showed superior performance compared to existing methods based on Symmetric Distance and Correlation Coefficient.
  • The method achieved high efficiency in terms of computational time and rationalized perception.

Conclusions:

  • The single physicochemical property-based representation and generalized NTV metric provide an effective and efficient approach for protein sequence comparison.
  • This method offers a valuable alternative for phylogenetic analysis, outperforming previous techniques in accuracy and efficiency.
  • The findings suggest broader applicability of this method in evolutionary and functional studies of proteins.