Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Evolutionary Relationships through Genome Comparisons02:54

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...
Leaky Scanning02:28

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 stands for...
Gene Evolution - Fast or Slow?02:05

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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

You might also read

Related Articles

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

Sort by
Same author

Functional divergence of duplicated genes results in a novel blast resistance gene Pi50 at the Pi2/9 locus.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·2015
Same author

Regulation of microtubule dynamics by DIAPH3 influences amoeboid tumor cell mechanics and sensitivity to taxanes.

Scientific reports·2015
Same author

Aberrant Functional Connectivity Architecture in Alzheimer's Disease and Mild Cognitive Impairment: A Whole-Brain, Data-Driven Analysis.

BioMed research international·2015
Same author

Alternative NF-κB Isoforms in the Drosophila Neuromuscular Junction and Brain.

PloS one·2015
Same author

Grape seed proanthocyanidin protects liver against ischemia/reperfusion injury by attenuating endoplasmic reticulum stress.

World journal of gastroenterology·2015
Same author

Serum Levels of Progranulin Are Closely Associated with Microvascular Complication in Type 2 Diabetes.

Disease markers·2015

Related Experiment Video

Updated: Jun 5, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Inferring an organism-specific optimal threshold for predicting protein coding regions in eukaryotes based on a

Shanglei Xu1, Nini Rao, Xi Chen

  • 1School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, People's Republic of China.

Biotechnology Letters
|January 15, 2011
PubMed
Summary

This study introduces a novel bootstrap algorithm to determine optimal thresholds for predicting protein-coding DNA sequences in eukaryotes. This method significantly improves prediction accuracy compared to using a universal threshold.

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

Related Experiment Videos

Last Updated: Jun 5, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Accurate identification of protein-coding sequences is crucial for eukaryotic genome analysis.
  • Existing prediction methods using power spectrum analysis are limited by the need for organism-specific thresholds.
  • Variability in gene structure across eukaryotes complicates the selection of a universal prediction threshold.

Purpose of the Study:

  • To develop a novel, organism-specific method for determining optimal thresholds in power spectrum analysis for predicting protein-coding regions in eukaryotes.
  • To enhance the accuracy of gene prediction by overcoming limitations of fixed empirical thresholds.

Main Methods:

  • A bootstrap algorithm was developed to infer organism-specific optimal thresholds.
  • The method requires minimal input: a few annotated protein-coding regions from the target organism.
  • Power spectrum analysis was employed for sequence discrimination.

Main Results:

  • The novel method achieved an average prediction accuracy of 81% on test datasets.
  • This represents a 19% improvement over the accuracy obtained using a fixed empirical threshold (P=4).
  • The organism-specific thresholds led to more precise discrimination between coding and non-coding DNA.

Conclusions:

  • The proposed bootstrap algorithm provides a simple and effective way to determine optimal thresholds for eukaryotic gene prediction.
  • This approach enhances the accuracy and reliability of predicting protein-coding regions across diverse eukaryotic genomes.
  • The method is broadly applicable and facilitates more accurate genomic annotation.