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Comparative Genomics: Introduction, Benefits, and Bioinformatics Tools

Comparative Genomics: Introduction, Benefits, and Bioinformatics Tools

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Introduction to Comparative Genomics

Comparative genomics is a branch of biology that compares the genomic characteristics of different life forms. The DNA sequence, genes, gene order, regulatory sequences, and other genomic structural landmarks are examples of genomic attributes. Whole or large portions of genomes leading from genome projects are evaluated in this branch of genomics to investigate basic biological commonalities and dissimilarities, as well as evolutionary interactions between organisms. Comparative genomics' main concept is that the general characteristics of two organisms are frequently encoded within their evolutionarily conserved DNA. As a result, comparative genomic methodologies begin with some type of genome sequence alignment, followed by a search for orthologous sequences (sequences that share a common ancestor) in the aligned genomes and a determination of how conserved those sequences are. On the basis of these, genome and molecular evolution can be inferred, which can then be placed in the context of, say, phenotypic evolution or population genetics.

Benefits of Comparative Genomics

Classifying DNA sequences that have been "conserved" - that is, preserved over millions of years in a variety of organisms - is a crucial move toward comprehending the genome itself. It identifies genes that are required for life and highlights genomic cues that regulate gene function in a variety of species. It allows us to learn more about how genes interact with different biological systems, which could lead to new ways to cure human illnesses and improve human health.

Comparative genomics is also an effective tool for researching evolution. Researchers can better comprehend how the appearance, behavior, and biology of life forms have changed over the years by taking the opportunity of - and evaluating - evolutionary connections between species and the corresponding distinctions in their DNA.

Comparative genomics is becoming more widely used in agriculture, biotechnology, and zoology as a platform to tease apart the frequently slight variations among animal species as DNA sequencing technology becomes more effective and cheaper. Such activities have resulted in new perspectives into some evolutionary branches, improved the health of domesticated animals, and pointed to new conservation techniques for rare and endangered species.

Results of Comparative Genomics

The findings of comparative genomics have been astounding. Comparative genomics is progressively being used by researchers to investigate topics ranging from human growth and actions to metabolism and illness susceptibility. These researches are revealing new behavioral, neurological, and developmental mechanisms as well as genes that are shared or related between species. Comparative genomics is being used by some scientists to uncover the genomic underpinnings of illness in animals in the hopes of learning more about disease advancement in humans.

Some Software and Tools Used in Comparative Genomics

Opscan 1:1 Ortholog Calling to Synteny with iAdhore
Opscan is a program that detects orthologous genes in two sets of genes, which is required for building synteny between species. Many other software programs, such as BLAST, OrthoMCL, OrthoFinder, and others, can offer ortholog calling capacities. Opscan, on the other hand, has some distinct advantages and is extremely fast.

GeneOverlap R package / Fisher's exact testing
A common bioinformatics experiment is to find genes that are noticeably correlated with an attribute or characteristic of a transcriptome/genome. This can be done quickly and easily with the GeneOverlap package.

Identifying the evolutionary origin of all genes in a genome
Phylostratr is a R package that creates phylostratigraphies for all genes in a genome. For a genome, you'll need full predicted proteins transcribed from transcripts. Please cite Phylostratr if you employ this application for your study.

About CD Genomics Bioinformatics Analysis

The bioinformatics analysis department of CD Genomics provides novel solutions for data-driven innovation aimed at discovering the hidden potential in biological data, tapping new insights related to life science research, and predicting new prospects.

References

  1. Maloy S, Hughes K, editors. Brenner's encyclopedia of genetics. Academic Press; 2013.
  2. Frazer KA, Pachter L, Poliakov A, et aI. VISTA: computational tools for comparative genomics. Nucleic acids research. 2004, 32(suppl_2).
  3. Hardison RC. Comparative genomics. PLoS Biol. 2003, 1(2).
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