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

Search research articles

Related Experiment Videos

Identifying chimerism in proteins using hidden Markov models of codon usage

L Hunter¹, B Zeeberg

¹National Library of Medicine, Bethesda, MD 20894, USA. hunter@nlm.nih.gov

Proceedings. International Conference on Intelligent Systems for Molecular Biology

|January 1, 1997

Summary

We developed a new method to detect chimeric proteins by analyzing codon usage differences in their nucleotide sequences. This approach aids in identifying proteins formed from multiple ancestral sequences, useful for genome-wide screening.

Related Concept Videos

You might also read

Related Articles

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

Sort by

Same author

Flow-Xl: a new facility for the analysis of crystallization in flow systems.

Journal of applied crystallography·2024

Same author

Impact of maternal body mass index (BMI) and the challenges of fetal echocardiography.

Public health·2024

Same author

Pulmonary hypertension in adults completing tuberculosis treatment.

African journal of thoracic and critical care medicine·2023

Same author

Effects and side effects of maternal administration of indomethacin for fetal tricuspid valve dysplasia.

Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology·2020

Same author

A comparison of trauma scoring systems for injuries presenting to a district-level urban public hospital in Western Cape.

South African journal of surgery. Suid-Afrikaanse tydskrif vir chirurgie·2020

Same author

Clinical and cost implications of using immediate MRI in the management of patients with a suspected scaphoid fracture and negative radiographs results from the SMaRT trial.

The bone & joint journal·2019

Area of Science:

Evolutionary biology
Genomics
Molecular biology

Background:

Protein chimerism involves combining ancestral sequences into single proteins.
Detecting chimeric proteins is crucial for understanding evolutionary processes.

Purpose of the Study:

To propose a novel computational method for identifying chimeric proteins.
To analyze nucleotide sequences for evidence of combined ancestral origins.

Main Methods:

Analyzing distributions of synonymous (isoaccepting) codons across protein regions.
Utilizing hidden Markov models (HMMs) to assess codon usage patterns.
Comparing model fits to natural sequences against randomized controls.

Main Results:

Related Experiment Videos

Demonstrated the method's efficacy on yeast amino-acyl tRNA synthetase families.
The approach successfully identified regional codon usage variations indicative of chimerism.

Conclusions:

The developed method offers a robust way to detect chimeric proteins.
This technique is suitable for automated screening of large genomic datasets.