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Evolutionary Relationships through Genome Comparisons

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...

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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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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.

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

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Updated: Jul 4, 2026

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Finding genes in genome sequence.

Alice Carolyn McHardy¹

¹IBM Thomas J. Watson Research Center, Yorktown Heights, NY, USA.

Methods in Molecular Biology (Clifton, N.J.)

|June 21, 2008

Summary

Automated gene finding identifies DNA sequences encoding proteins and RNAs. This crucial first step in genomic analysis is essential for understanding biological functions across diverse genomes.

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Gene finding is the critical initial step in analyzing genomic sequences.
Accurate gene identification is fundamental for all subsequent downstream analyses.
Understanding gene structures is key to deciphering biological functions.

Purpose of the Study:

To describe the biological basis of gene finding.
To review computational approaches and software for automated gene identification.
To present the state-of-the-art in gene finding for various genomic contexts.

Main Methods:

Focus on the biological principles underlying gene identification.
Examination of computational algorithms and methodologies for gene prediction.

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Last Updated: Jul 4, 2026

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

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

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

Published on: May 28, 2021

Evaluation of existing software tools for automated gene finding.

Main Results:

Comprehensive overview of automated protein-coding gene identification.
Description of methods applicable to prokaryotic and eukaryotic genomes.
Inclusion of approaches for novel multi-species environmental sequence data.

Conclusions:

Automated gene finding is a vital component of genomic research.
The described methods and tools advance the analysis of diverse genomic data.
State-of-the-art gene finding enables comprehensive biological interpretation.