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

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

6.4K
Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
6.4K
RNA-seq03:21

RNA-seq

9.9K
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...
9.9K
Next-generation Sequencing03:00

Next-generation Sequencing

88.4K
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....
88.4K
Sanger Sequencing01:57

Sanger Sequencing

753.8K
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...
753.8K

You might also read

Related Articles

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

Sort by
Same author

IQ-TREE 3: phylogenomic inference software using complex evolutionary models.

Molecular biology and evolution·2026
Same author

Rate variation and recurrent sequence errors in pandemic-scale phylogenetics.

Nature methods·2026
Same author

Assessing phylogenetic confidence at pandemic scales.

Nature·2025
Same author

Highly Recurrent Multinucleotide Mutations in SARS-CoV-2.

Molecular biology and evolution·2025
Same author

Raman identification of single nucleotides flowing through permeable plasmonic films.

Nature communications·2025
Same author

Detecting Interspecific Positive Selection Using Convolutional Neural Networks.

Molecular biology and evolution·2025

Related Experiment Video

Updated: Jun 12, 2025

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

3.3K

A generalized protein identification method for novel and diverse sequencing technologies.

Bikash Kumar Bhandari1, Nick Goldman1

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.

NAR Genomics and Bioinformatics
|September 19, 2024
PubMed
Summary

New hidden Markov model methods enable accurate protein identification from noisy sequencing data. This approach works even with early devices that have limited amino acid discrimination, improving protein discovery.

More Related Videos

Identification of Antibacterial Immunity Proteins in Escherichia coli using MALDI-TOF-TOF-MS/MS and Top-Down Proteomic Analysis
09:26

Identification of Antibacterial Immunity Proteins in Escherichia coli using MALDI-TOF-TOF-MS/MS and Top-Down Proteomic Analysis

Published on: May 23, 2021

3.1K
Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling
09:35

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Published on: April 1, 2017

13.8K

Related Experiment Videos

Last Updated: Jun 12, 2025

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

3.3K
Identification of Antibacterial Immunity Proteins in Escherichia coli using MALDI-TOF-TOF-MS/MS and Top-Down Proteomic Analysis
09:26

Identification of Antibacterial Immunity Proteins in Escherichia coli using MALDI-TOF-TOF-MS/MS and Top-Down Proteomic Analysis

Published on: May 23, 2021

3.1K
Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling
09:35

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Published on: April 1, 2017

13.8K

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Genomics

Background:

  • Protein sequencing technology is advancing rapidly, but early devices produce noisy and error-prone data.
  • Current methods struggle with identifying proteins from incomplete or inaccurate sequence signatures.

Purpose of the Study:

  • To develop a broadly applicable method for protein identification using noisy sequence data from next-generation sequencers.
  • To assess the performance of this method across various simulated sequencing error conditions.

Main Methods:

  • A hidden Markov model (HMM) was developed to analyze protein signatures with potential errors.
  • The HMM method was tested on a human protein database (N=20,181) using a hypothetical sequencing device simulating novel technologies.

Main Results:

  • The HMM method demonstrated good performance in identifying proteins under diverse conditions, including varying signal resolvability and error rates (insertions, deletions).
  • High accuracy was achieved even with limited amino acid discrimination and fragmented sequence data.

Conclusions:

  • The developed hidden Markov model method enables accurate protein identification from noisy sequence data, even with early sequencing devices.
  • This approach is expected to be valuable for a wide range of future protein sequencing technologies and applications.