Related Experiment Video
Updated: Jun 24, 2026
09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes
Micah Hamady1, Stephanie A Wilson, Jesse Zaneveld
1Department of Computer Science, University of Colorado, Boulder, CO 80309, USA.
Bioinformatics (Oxford, England)
|March 13, 2009
Summary
CodonExplorer is a new online tool for analyzing DNA composition and codon usage across millions of genes. It helps researchers explore factors driving gene evolution and identify genes with high expression or horizontal transfer.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- DNA composition and codon usage are fundamental to understanding gene function, evolution, and expression.
- Identifying genes with specific compositional properties can reveal insights into their biological roles and evolutionary history.
Purpose of the Study:
- To introduce CodonExplorer, an online tool and interactive database for exploring DNA composition and codon usage.
- To enable rapid investigation of factors influencing gene and genome compositional evolution.
- To facilitate the identification of genes with characteristics indicative of high expression or horizontal gene transfer.
Main Methods:
- Utilizes an extensive online database containing millions of genes.
- Employs analysis of GC content and codon usage frequency.
- Provides interactive exploration capabilities.
Main Results:
- CodonExplorer allows for the rapid exploration of gene and genome compositional evolution.
- The tool effectively exploits GC content and codon usage frequency.
- It successfully identifies genes with compositions suggestive of high expression or horizontal transfer.
Conclusions:
- CodonExplorer is a valuable resource for researchers studying gene function and evolution.
- The tool aids in understanding the evolutionary pressures on DNA composition.
- It offers a novel approach to identifying genes with specific functional or evolutionary implications.
Related Concept Videos
02:54Evolutionary 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...
02:26Comparing 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%...
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%...
02:16Comparing 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...
02:02Genomics
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...
03:21RNA-seq
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
03:00Next-generation Sequencing
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.