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Related Concept Videos

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

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 DNA...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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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.
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Conservation of Protein Domains02:26

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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 form...
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...

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Related Experiment Video

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Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

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Published on: February 10, 2023

Tree Gibbs Sampler: identifying conserved motifs without aligning orthologous sequences.

Xiaohui Cai1, Haiyan Hu, Xiaoman Shawn Li

  • 1Division of Biostatistics, School of Medicine, Indiana University, Indianapolis, IN 46202, USA.

Bioinformatics (Oxford, England)
|June 2, 2007
PubMed
Summary

Tree Gibbs Sampler identifies DNA motifs using evolutionary conservation and overrepresentation. This tool aids in discovering regulatory elements across diverse species without needing pre-aligned sequences.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Identifying regulatory elements is crucial for understanding gene regulation.
  • Existing methods often require pre-aligned orthologous sequences, limiting their applicability.
  • The Tree Gibbs Sampler software addresses these limitations.

Purpose of the Study:

  • To introduce the Tree Gibbs Sampler software for motif discovery.
  • To highlight its ability to identify motifs using both overrepresentation and evolutionary conservation properties.
  • To demonstrate its utility in analyzing multiple genomes without pre-alignment.

Main Methods:

  • The Tree Gibbs Sampler employs a probabilistic approach.
  • It integrates motif overrepresentation with phylogenetic information.
  • The algorithm does not rely on pre-aligned orthologous sequences.

Main Results:

  • The software successfully identifies functional motifs.
  • It is effective across genomes of varying evolutionary distances.
  • Enables motif discovery in non-model organisms.

Conclusions:

  • Tree Gibbs Sampler is a versatile tool for motif identification.
  • It facilitates the discovery of regulatory elements in diverse genomic contexts.
  • Its independence from pre-aligned sequences broadens its applicability in comparative genomics.