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 Experiment Video

Updated: Jun 28, 2026

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
11:02

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Published on: October 18, 2013

SHMTool: a webserver for comparative analysis of somatic hypermutation datasets.

Thomas Maccarthy1, Sergio Roa, Matthew D Scharff

  • 1Dept of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA.

DNA Repair
|October 28, 2008
PubMed
Summary

Somatic hypermutation (SHM) analysis is complex due to varied datasets and lack of standardization. SHMTool offers a standardized webserver for comparing SHM data, simplifying analysis of antibody diversity generation.

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

Genetically driven immune microenvironment states associate with therapeutic responses in MYD88 mutant lymphomas.

Molecular cancer·2026
Same author

Integrated Single-Cell and Spatial Multi-Omics of Clonal Precursors and Immune Niches in Germinal Center Lymphomas.

Cancers·2026
Same author

Exon Targeted Retrieval and Classification Toolbox (ExTRaCT): a gene search pipeline to find APOBEC3 Z-domains in novel bat genomes.

bioRxiv : the preprint server for biology·2026
Same author

HDAC7 is a key factor for the germinal center reaction and its underexpression is associated with DLBCL prognosis.

Journal of immunology (Baltimore, Md. : 1950)·2026
Same author

Network divergence analysis identifies adaptive gene modules and two orthogonal vulnerability axes in pancreatic cancer.

Molecular oncology·2026
Same author

An extensive study of two-node McCulloch-pitts networks.

Journal of theoretical biology·2026

Area of Science:

  • Immunology
  • Molecular Biology
  • Bioinformatics

Background:

  • Somatic hypermutation (SHM) is crucial for generating antibody diversity.
  • Existing SHM datasets are difficult to compare due to non-standardized analyses.
  • Genetic defects in repair mechanisms also impact SHM, complicating comparisons.

Purpose of the Study:

  • To develop a standardized method for analyzing and comparing somatic hypermutation datasets.
  • To introduce SHMTool, a webserver designed to facilitate SHM data analysis.

Main Methods:

  • Development of a webserver (SHMTool) for SHM data analysis.
  • Implementation of standardized criteria for base composition correction and unique mutation inclusion.
  • Facilitation of comparative analysis across different SHM datasets.

More Related Videos

Introductory Analysis and Validation of CUT&RUN Sequencing Data
04:58

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

Related Experiment Videos

Last Updated: Jun 28, 2026

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
11:02

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Published on: October 18, 2013

Introductory Analysis and Validation of CUT&RUN Sequencing Data
04:58

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

Main Results:

  • SHMTool provides a standardized platform for SHM dataset comparison.
  • The tool addresses challenges in comparing studies due to variations in analytical criteria.
  • It simplifies the time-consuming process of analyzing large mutation datasets.

Conclusions:

  • SHMTool enables standardized and efficient comparison of somatic hypermutation data.
  • This standardization aids in understanding antibody diversity generation across studies.
  • The webserver is a valuable resource for researchers in immunology and molecular biology.