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

You might also read

Related Articles

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

Sort by
Same author

Development and Validation of an m6A-Derived Prognostic Signature in Lung Adenocarcinoma.

Journal of Cancer·2026
Same author

Whole genome sequencing in oesophageal adenocarcinoma unmasks potential precision therapies.

BMC cancer·2026
Same author

Enhanced measures of neoantigenicity capture unique tumor-immune interactions across primary melanoma subtypes.

Genome medicine·2026
Same author

Explainable machine learning identifies features and thresholds predictive of immunotherapy response.

Scientific reports·2026
Same author

Cancer genome standards for long-read sequencing using cancer cell line mixtures.

GigaScience·2026
Same author

Multi-omics reveals key molecular and cellular features of advanced small cell lung cancers associated with distinct therapeutic opportunities.

Genome medicine·2026
Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026
Same journal

KASSPer: Kinase Active Site Structure Prediction using Protein and Ligand Language Models and Its Application to Virtual Screening.

Bioinformatics (Oxford, England)·2026
Same journal

IDR searcher: a search engine solution for public image resources.

Bioinformatics (Oxford, England)·2026
Same journal

KCFtools: Rapid alignment-free method for introgression screening and GWAS using k-mer profiles.

Bioinformatics (Oxford, England)·2026
Same journal

Meta2DB: Curated shotgun metagenomic feature sets and metadata for health state prediction.

Bioinformatics (Oxford, England)·2026
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Jun 5, 2026

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
09:14

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

X-MATE: a flexible system for mapping short read data.

David L A Wood1, Qinying Xu, John V Pearson

  • 1The University of Queensland, Queensland, Australia.

Bioinformatics (Oxford, England)
|January 11, 2011
PubMed
Summary
This summary is machine-generated.

Accurate genome mapping is crucial for biological discovery. X-MATE is an updated pipeline that improves RNA-Seq and DNA dataset mapping with enhanced performance and flexibility.

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

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells
06:02

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

Published on: October 28, 2025

Related Experiment Videos

Last Updated: Jun 5, 2026

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
09:14

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

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

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells
06:02

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

Published on: October 28, 2025

Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Accurate genome mapping is essential for biological discovery and statistical prediction.
  • Previous RNA-Seq mapping pipelines like RNA-MATE have been developed.
  • The increasing volume of genome re-sequencing data necessitates advanced mapping tools.

Purpose of the Study:

  • To present X-MATE, an updated bioinformatics pipeline.
  • To enhance the mapping of both RNA-Seq and DNA sequencing datasets.
  • To improve performance, output formats, and flexibility of core mapping software.

Main Methods:

  • X-MATE is an updated version of the RNA-MATE pipeline.
  • It incorporates advancements in mapping software and file formats.
  • The pipeline offers improved performance and flexibility in core mapping tools.

Main Results:

  • X-MATE demonstrates enhanced capabilities for mapping RNA-Seq and DNA datasets.
  • The pipeline features improved performance and output file formats.
  • X-MATE provides greater flexibility in core mapping software selection.

Conclusions:

  • Accurate and complete mapping of sequencing data to a reference genome significantly enhances biological discovery.
  • X-MATE offers an improved and more flexible solution for mapping both RNA-Seq and DNA datasets.
  • The updated pipeline supports the growing needs of genome re-sequencing projects.