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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

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...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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...
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...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

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An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

CASSIOPE: an expert system for conserved regions searches.

Virginie Lopez Rascol1, Anthony Levasseur, Olivier Chabrol

  • 1EBM UMR 6632 LATP, 3 place V Hugo - 13 331 Marseille cedex 03 France. virginie.lopez-rascol@univ-provence.fr

BMC Bioinformatics
|September 11, 2009
PubMed
Summary

CASSIOPE is a new system that automates the identification of conserved genomic regions across multiple species. This tool aids in understanding genome evolution and identifying important genetic elements.

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Comparative genomics and conserved chromosomal region analysis are crucial for understanding genome evolution and biological systems.
  • Identifying conserved regions aids in clarifying genome evolution, detecting quantitative trait loci (QTLs), and investigating gene function.
  • Genome-scale conserved region identification is computationally intensive, necessitating automated processes.

Purpose of the Study:

  • To develop an automated system for identifying statistically significant conserved regions across multiple genomes.
  • To address the computational challenges in comparative genomics by providing an efficient and automated solution.
  • To integrate phylogenetic analysis and statistical testing for robust detection of conserved gene clusters.

Main Methods:

  • Developed CASSIOPE (Clever Agent System for Synteny Inheritance and Other Phenomena in Evolution), a modular system on a multi-agent framework.
  • Implemented automated phylogenies and statistical testing to identify conserved regions.
  • Applied the system to 19 species for conserved region analysis.

Main Results:

  • CASSIOPE successfully identified 1,561 statistically significant conserved regions across 19 species.
  • The system integrates evolutionary biology concepts, automated phylogenies, and statistical testing.
  • CASSIOPE is presented as the first system to meet all key requirements for genome-scale conserved region identification.

Conclusions:

  • CASSIOPE enables the study of conserved regions and inference of conserved gene clusters using phylogenies and statistical significance tests.
  • The system facilitates research into genome evolution and gene function.
  • Source code for CASSIOPE is freely available.