Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

From DNA to Protein

From DNA to Protein

The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...

The Central Dogma

The Central Dogma

The Central Dogma

The Central Dogma

The central dogma explains the flow of genetic information from DNA nucleotides to the amino acid sequence of proteins.
RNA is the Missing Link Between DNA and Proteins
In the early 1900s, scientists discovered that DNA stores all the information needed for cellular functions and that proteins perform most of these functions. However, the mechanisms of converting genetic information into functional proteins remained unknown for many years. Initially, it was believed that a single gene is...

Leaky Scanning

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...

Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

Prokaryotic Gene Structure and Organization

Prokaryotic Gene Structure and Organization

Prokaryotic genomes exhibit a streamlined organization of coding and non-coding regions essential for gene expression and protein synthesis. While coding regions contain the genetic instructions for proteins or functional RNAs, non-coding regions regulate the precise transcription and translation of these genes.Coding Regions: Proteins and RNAsThe primary coding regions, known as structural genes, include sequences transcribed into messenger RNA (mRNA) and ultimately translated into...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026

Same author

Unlocking precision diagnostics: A multimodal framework integrating metabolomics with advanced machine learning techniques.

PloS one·2026

Same author

Quantum coherence stabilization in biology via feedback with coherent background fields.

Electromagnetic biology and medicine·2026

Same author

Effects of acetylation on human insulin structure, and dynamics at different temperatures: A molecular dynamics simulation study.

Journal of biosciences·2026

Same author

Modeling optimal timing of immunotherapy and chemotherapy to prevent resistance and recurrence in triple-negative breast cancer.

Scientific reports·2026

Same author

Boolean logic links chromatin accessibility states to gene expression variability across cell types.

Nucleic acids research·2026

Same journal

CNV-ECOD: A copy number variation detection method based on ECOD algorithm using next-generation sequencing data.

Journal of bioinformatics and computational biology·2026

Same journal

ReinVar: A model-free paradigm-based reinforcement learning approach to detect copy number variation.

Journal of bioinformatics and computational biology·2026

Same journal

When pipelines run but coordinates fail: A simple spatial specificity check for false locality in post-GWAS analysis.

Journal of bioinformatics and computational biology·2026

Same journal

Comparative benchmarking of template-based, evolutionary-diffusion, and generative language models for IsPETase structure prediction.

Journal of bioinformatics and computational biology·2026

Same journal

Trap spaces as labelled ideals of SCC posets: A structural-functional theory of reachability in asynchronous boolean networks.

Journal of bioinformatics and computational biology·2026

Same journal

Erratum - DDINet: Drug-drug interaction prediction network based on multi-molecular fingerprint features and multi-head attention centered weighted autoencoder.

Journal of bioinformatics and computational biology·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Apr 20, 2026

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

Published on: August 1, 2016

Codon usage and protein sequence pattern dependency in different organisms: A Bioinformatics approach.

Mohammad-Hadi Foroughmand-Araabi¹, Bahram Goliaei, Kasra Alishahi

¹Department of Mathematical Sciences, Sharif University of Technology, Tehran, Iran.

Journal of Bioinformatics and Computational Biology

|November 21, 2014

Summary

This summary is machine-generated.

Protein sequence patterns influence codon usage in related genes, impacting gene regulation and protein levels. This study reveals a novel mechanism linking specific protein motifs to synonymous codon selection for functional control.

Keywords:

Codon usage logistic regression model protein sequence pattern protein translation efficiency

More Related Videos

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Published on: June 24, 2019

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Related Experiment Videos

Last Updated: Apr 20, 2026

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

Published on: August 1, 2016

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Published on: June 24, 2019

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

Genetics
Molecular Biology
Bioinformatics

Background:

Synonymous codon usage is non-random, but its role in gene regulation remains unclear.
Previous research explored links between codon usage and gene regulation, translation efficiency, mRNA stability, and protein domains.
A universal codon usage mechanism for gene regulation has been recently proposed.

Purpose of the Study:

To investigate the influence of protein sequence patterns on codon usage in related genes.
To develop a statistical model that incorporates protein patterns to explain codon usage preferences.
To determine if codon usage controls protein levels for functionally related genes.

Main Methods:

Analysis of codon usage patterns in gene subsequences corresponding to specific protein motifs.
Development of a multinomial logistic regression model to assess the effect of protein patterns on codon usage.
Comparison of the proposed model against traditional organism-dependent codon usage models.

Main Results:

Specific ratios of synonymous codons are associated with gene parts translated into protein subsequences matching defined patterns.
The developed statistical model provides a better explanation for observed codon usage preferences than classic models.
Codon usage was found to play a role in controlling protein levels for genes involved in specific biological functions.

Conclusions:

Protein sequence patterns are a significant factor influencing synonymous codon usage.
This study presents a novel finding that codon usage contributes to regulating protein levels in functionally related genes.
The proposed model offers improved insights into the mechanisms of gene regulation via codon usage.