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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...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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.
Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

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Related Experiment Video

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

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Comparing thousands of circular genomes using the CGView Comparison Tool.

Jason R Grant1, Adriano S Arantes, Paul Stothard

  • 1Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada.

BMC Genomics
|May 25, 2012
PubMed
Summary

The CGView Comparison Tool (CCT) enables visual comparison of new genomes against thousands of existing ones. This bioinformatics tool aids in identifying novel sequences and evolutionary insights through customizable graphical maps.

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Advances in sequencing technology are generating vast numbers of small genomes.
  • Whole-genome comparisons are crucial for understanding organismal biology and evolution.
  • Existing visualization tools lack features for comparing new genomes to large existing sequence collections.

Purpose of the Study:

  • To develop a novel tool for efficient and comprehensive whole-genome comparisons.
  • To provide advanced visualization capabilities for genomic analysis.
  • To overcome limitations of existing genome comparison software.

Main Methods:

  • The CGView Comparison Tool (CCT) uses BLAST for sequence comparisons.
  • It generates interactive graphical maps displaying sequence features, gene names, and composition.
  • CCT supports comparisons against entire genome collections and allows extensive customization.

Main Results:

  • CCT visually compares reference sequences to thousands of genomes on a desktop computer.
  • Generated maps integrate sequence conservation, functional classifications, and compositional data.
  • The tool can produce high-resolution maps (e.g., 400 Megapixel) suitable for large-format printing.

Conclusions:

  • CCT offers unique analysis and visualization functionalities for circular genomes.
  • It facilitates the identification of rapidly evolving or horizontally transferred sequences.
  • The tool aids in discovering unusual functional properties in newly sequenced genomes.