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Related Concept Videos

Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
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...
Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...

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Updated: Jun 24, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Fast structural search in phylogenetic databases.

Jason T L Wang1, Huiyuan Shan, Dennis Shasha

  • 1Department of Computer Science, New Jersey Institute of Technology, University Heights, Newark, NJ, USA. wangj@njit.edu

Evolutionary Bioinformatics Online
|March 28, 2009
PubMed
Summary
This summary is machine-generated.

Searching large phylogenetic databases for similar tree structures is challenging. This study introduces efficient structural search techniques and a filtering method to find closely matching phylogenetic trees, improving database search capabilities.

Keywords:
Structural pattern matchingphylogenetic treesstructural search and retrievaltree search strategies

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Last Updated: Jun 24, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

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Published on: August 14, 2018

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16:17

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Phylogenetics

Background:

  • Phylogenetic databases are rapidly expanding, necessitating efficient search functionalities.
  • Current search methods in these databases primarily focus on attribute or text-based queries.
  • Searching by topological or physical tree structure, particularly for approximate matches in large datasets, remains a significant challenge.

Purpose of the Study:

  • To develop novel structural search techniques for phylogenetic databases.
  • To enable efficient searching for trees that are topologically or structurally similar to a query pattern.
  • To address the limitations of existing methods for large-scale, approximate structural searches in phylogenies.

Main Methods:

  • Proposed structural search algorithms designed for both rooted and unrooted phylogenetic trees.
  • Incorporated a filtering technique to accelerate the search process within large databases.
  • Defined a 'closeness' measure based on shared topological relationships between query and database trees.

Main Results:

  • Developed and presented algorithms applicable to weighted and unweighted phylogenetic trees.
  • Experimental results validated the proposed similarity measure against existing tree metrics.
  • Demonstrated the efficiency of the filtering and search techniques on large phylogenetic datasets.

Conclusions:

  • The proposed structural search techniques offer a promising approach for efficiently querying large phylogenetic databases.
  • The methods effectively identify trees with similar topological structures, addressing a key limitation in current database search capabilities.
  • The developed approach enhances the ability to perform approximate structural searches in phylogenetics.