Comparative Genomics Analysis

BioCodeKb - Bioinformatics Knowledgebase

Comparative genomics is the comparison of biological information derived from whole-genome sequences.


Comparative genomics is playing major role in extracting useful information from biological sequences. One important aspect of comparative genomics is the comparison of proteomes (the complete protein set) of two or more organisms. In addition, it involves the comparison of gene locations, relative gene order, and regulation.


Importance of Comparative Genome Analysis

  • Comparative genomics helps in selecting model organisms

  • provides a powerful way to distinguish regulatory motifs from non-functional patterns based on their conservation

  • Helps in gene finding

  • helpful for studying evolution and variation

  • Comparative analysis of genomes of individuals with genetic disease against healthy individuals may show clues of eliminating that disease

  • Provides a highly detailed view of how organisms are related to each other at the genetic level

  • Agriculture is a field that reaps the benefits of comparative genomics. Identifying the loci of advantageous genes is a key step in breeding crops that are optimized for greater yield, cost-efficiency, quality, and disease resistance

  • Comparative genomics can also be used to generate specificity for vaccines against pathogens that are closely related to commensal microorganisms

  • In an approach known as reverse vaccinology, researchers can discover candidate antigens for vaccine development by analyzing the genome of a pathogen or a family of pathogens

  • helps in the clustering of regulatory sites


Comparative genomic methods have allowed researchers to gather information about genetic variation, differential gene expression, and evolutionary dynamics in primates that were indiscernible using previous data and methods.


Comparative genomics has a root in the comparison of virus genomes in the early 1980s. For example, small RNA viruses infecting animals (picornaviruses) and those infecting plants (cowpea mosaic virus) were compared and turned out to share significant sequence similarity and, in part, the order of their genes.


A simple comparison of the general features of genomes such as genome size, number of genes, and chromosome number presents an entry point into comparative genomic analysis. The comparisons highlight some striking findings.


Comparative genomics involves the examination and comparison of sequence, genes and regulatory regions between different organisms. Next generation sequencing of different organisms allows for a better understanding of the structure and function of genes and helps to identify those that are unique and those that are conserved among species. Comparisons of discrete segments of the genome is possible by alignment of homologous DNA between species. These alignments also help researchers identify signals that represent the location of genes and the sequences that regulate gene expression.


Several comparative genome tools have been developed to allow users to search for:

  1. horizontally transferred genes

  2. conservation of synteny groups

  3. pan-genome sizes and their evolution for a set of genes

  4. common and variable proportions of each genome

  5. variable genome and strain specific sequences, annotations


Some useful browsers that give us information about the comparative genomic analysis are;

  • UCSC Browser

  • Ensembl

  • MapView

  • VISTA

  • BlueJay Genome Browser

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