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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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 form...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

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Updated: May 13, 2026

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Using protein clusters from whole proteomes to construct and augment a dendrogram.

Yunyun Zhou1, Douglas R Call, Shira L Broschat

  • 1School of Electrical Engineering and Computer Science, Washington State University, P.O. Box 642752, Pullman, WA 99164-2752, USA.

Advances in Bioinformatics
|March 20, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces a novel ab initio method for building phylogenetic trees using protein clusters, enabling relationship estimations across thousands of species. The pClust software and Smith-Waterman algorithm enhance accuracy in constructing these species relationship dendrograms.

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Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry
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Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Published on: November 12, 2012

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Phylogenetic tree construction is crucial for understanding evolutionary relationships.
  • Existing methods may have limitations in accuracy and scalability for large datasets.
  • Metagenomic studies require efficient tools for analyzing vast amounts of protein sequence data.

Purpose of the Study:

  • To present a new ab initio approach for constructing unrooted dendrograms using protein clusters.
  • To estimate evolutionary relationships among thousands of species based on their proteomes.
  • To utilize and demonstrate the pClust software for phylogenetic analysis.

Main Methods:

  • Employed the open-source pClust software for protein cluster generation.
  • Utilized the Smith-Waterman algorithm for optimal sequence alignment, ensuring high accuracy.
  • Developed protein profiles and a correlation filter library for dendrogram construction and augmentation.
  • Used BLASTp to create profiles for new taxa to integrate them into the dendrogram.

Main Results:

  • Successfully generated an unrooted dendrogram using protein clusters from 527 bacterial plasmid proteomes.
  • Demonstrated the utility of the insertion algorithm by augmenting the dendrogram with twelve pAKD plasmids.
  • The Smith-Waterman algorithm in pClust provided greater accuracy compared to BLAST-based methods.

Conclusions:

  • The presented ab initio approach offers a scalable and accurate method for phylogenetic tree construction.
  • pClust and the developed methodology are valuable tools for analyzing large-scale proteomic data, particularly in metagenomics.
  • This method has significant potential for estimating relationships among thousands of species.