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

High-Resolution Mass Spectrometry (HRMS)

High-Resolution Mass Spectrometry (HRMS)

The resolution of a mass spectrometer depends on the efficiency of separating ions with different ion masses. The mass of an atom is approximated to the sum of the masses of protons and neutrons inside, considering the masses of protons and neutrons as equal. However, the masses of the proton (1.6726 × 10−24 g) and neutron (1.6749 × 10−24 g) are not truly equal. There is a minor error in the expression of atomic masses relative to the simplest atom of hydrogen. For...

You might also read

Related Articles

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

Sort by

Same author

Wistar rat model experiments for increasing intraocular pressure: a systematic review.

Daru : journal of Faculty of Pharmacy, Tehran University of Medical Sciences·2026

Same author

ERGA-BGE reference genome of <i>Gambusia holbrooki</i>, a globally invasive freshwater fish.

Open research Europe·2026

Same author

Exploring the Scope and Status of Biological Interventions in Malaria Control.

The American journal of tropical medicine and hygiene·2026

Same author

Single-cell systems network and machine learning dissection of ferroptosis in recurrent glioblastoma highlights astrocytic ZFP36 as a therapeutic hub for network medicine repurposing.

European journal of cancer (Oxford, England : 1990)·2026

Same author

Protocol for Effectiveness of Silver Diamine Fluoride in Arresting Caries in 3-6-year-old Children: A Community-Based Randomized Control Trial.

Journal of pharmacy & bioallied sciences·2026

Same author

Seroprevalence of chikungunya virus infection in East Delhi over a decade: A retrospective study.

Tropical doctor·2026

Same journal

Modulation of brain-kidney crosstalk by olanzapine in aluminum chloride-induced memory impairment: a preclinical investigation.

BMC research notes·2026

Same journal

Tagged and untagged amyloid precursor protein E2 domain have comparable thermal stability and metal-ion binding propensity.

BMC research notes·2026

Same journal

Phenotypical and functional characterization of a HepG2 cell clone stably overexpressing cytochrome P450 (CYP) 2C9.

BMC research notes·2026

Same journal

Inefficacy of a novel osmotic associative learning assay in C. elegans.

BMC research notes·2026

Same journal

Anticancer proteasome inhibitors are detrimental to the growth of Toxoplasma gondii in vitro.

BMC research notes·2026

Same journal

Body mass index, nutritional knowledge, and eating attitudes in dancer and non-dancer students.

BMC research notes·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Apr 26, 2026

A Mass Spectrometry-Based Proteomics Approach for Global and High-Confidence Protein R-Methylation Analysis

A Mass Spectrometry-Based Proteomics Approach for Global and High-Confidence Protein R-Methylation Analysis

Published on: April 28, 2022

HMM-ModE: implementation, benchmarking and validation with HMMER3.

Swati Sinha, Andrew Michael Lynn¹

¹School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India. andrew@jnu.ac.in.

BMC Research Notes

|July 31, 2014

Summary

This summary is machine-generated.

HMM-ModE, upgraded with HMMER3, enhances protein sequence functional annotation by accurately differentiating protein folds and families. This computational method significantly reduces false positives, improving classification accuracy for large-scale projects.

More Related Videos

Detection of Copy Number Alterations Using Single Cell Sequencing

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

Related Experiment Videos

Last Updated: Apr 26, 2026

A Mass Spectrometry-Based Proteomics Approach for Global and High-Confidence Protein R-Methylation Analysis

A Mass Spectrometry-Based Proteomics Approach for Global and High-Confidence Protein R-Methylation Analysis

Published on: April 28, 2022

Detection of Copy Number Alterations Using Single Cell Sequencing

Detection of Copy Number Alterations Using Single Cell Sequencing

Published on: February 17, 2017

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

Area of Science:

Computational biology
Bioinformatics
Genomics

Background:

HMM-ModE is a computational method for generating family-specific profile Hidden Markov Models (HMMs) using negative training sequences.
It optimizes discrimination thresholds and modifies emission probabilities to reduce common fold-based signals.
The original protocol relied on HMMER for profile building and database searching.

Purpose of the Study:

To upgrade HMM-ModE to leverage the speed and probabilistic inference capabilities of HMMER3.
To improve the accuracy and efficiency of protein sequence functional annotation.
To benchmark the performance of the upgraded HMM-ModE against its previous version and other classification methods.

Main Methods:

Rewriting existing scripts for HMM profile parsing and emission probability modification to be compatible with HMMER3.
Utilizing HMMER3's enhanced database search speed for large-scale deployment.
Benchmarking the upgraded HMM-ModE using a gold standard set of protein families and a dataset of G protein-coupled receptors (GPCRs).

Main Results:

The upgraded HMM-ModE, utilizing HMMER3, demonstrates significant improvements in computational speed.
A marked reduction in false positive hits compared to default HMM profiles was observed.
Implementation on GPCR sequences showed improved classification accuracy across different hierarchical levels compared to existing methods.

Conclusions:

The new version of HMM-ModE is a highly specific method for differentiating protein fold (superfamily) and function (family) specific signals.
It aids in the functional annotation of protein sequences by providing accurate sub-family classification.
Modified profile HMMs of GPCR sequences offer a simple yet highly specific approach for family classification, even with shared physicochemical characteristics.