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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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...
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
Gene Conversion02:08

Gene Conversion

Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
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...

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Related Experiment Video

Updated: Jun 28, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

Syntenator: multiple gene order alignments with a gene-specific scoring function.

Christian Rödelsperger1, Christoph Dieterich

  • 1Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, Tübingen, Germany. christian.roedelsperger@charite.de

Algorithms for Molecular Biology : AMB
|November 8, 2008
PubMed
Summary
This summary is machine-generated.

Syntenator identifies conserved synteny across genomes using gene order, even for distantly related species. This novel approach surpasses nucleotide-level comparisons and existing methods for comparative genomics.

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Related Experiment Videos

Last Updated: Jun 28, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Area of Science:

  • Genomics
  • Bioinformatics
  • Comparative Genomics

Background:

  • Comparative genomics relies on identifying homologous regions and conserved syntenies.
  • Traditional methods like WABA and blastz focus on nucleotide-level alignments.
  • Conserved syntenies, defined by conserved gene orders, can be detected even between distantly related genomes.

Purpose of the Study:

  • To present a novel computational approach for identifying conserved synteny regions across multiple genomes.
  • To overcome limitations of nucleotide-level comparisons in detecting homology between distantly related genomes.

Main Methods:

  • Genomes and their alignments are represented as partial order graphs (POGs).
  • A dynamic programming approach with a gene-specific scoring function, reflecting protein sequence similarity, is used for POG alignment.
  • The method aligns gene orders to identify homologous regions.

Main Results:

  • The novel method consistently identifies larger homologous regions compared to nucleotide-level alignments.
  • Syntenator outperforms methods relying on predefined homology gene sets, successfully reproducing 80% of EnsEMBL human-mouse conserved syntenic blocks.
  • The approach effectively resolves orthology relations, particularly for remotely related and multiple genomes (up to 75% of 1:many and 27% of many:many relations).

Conclusions:

  • Syntenator is proposed as a robust software solution for inferring conserved syntenies among distantly related genomes.
  • The software facilitates advanced comparative genomics by leveraging gene order information.
  • Availability of the software is provided for broader research application.