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

The Open Materials 2024 (OMat24) inorganic materials dataset and models.

Nature computational science·2026
Same author

Validation of a machine learning model for predicting early deterioration in the emergency department.

The American journal of emergency medicine·2026
Same author

Ankh-Score Produces Better Sequence Alignments Than AlphaFold3.

Proteins·2026
Same author

Open Molecular Crystals 2025 (OMC25) dataset and models.

Scientific data·2026
Same author

Protein embeddings and local alignments.

Computational and structural biotechnology journal·2026
Same author

The Utility of Mucin 2 and Caudal-Type Homeobox Transcription Factor 2 Expression in the Diagnosis of Barrett's Esophagus: A Community-Based Study of Wide-Area Transepithelial Sampling and Forceps Biopsies.

The American journal of gastroenterology·2026
Same journal

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

Bioinformatics (Oxford, England)·2026
Same journal

SpaMFG: a Spatial Multi-omics Integration Method based on Feature Grouping.

Bioinformatics (Oxford, England)·2026
Same journal

CSCN: Inference of Cell-Specific Causal Networks Using Single-Cell RNA-Seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

Sparse CCA-Based Mediation Analysis with High-Dimensional Exposures and Mediators.

Bioinformatics (Oxford, England)·2026
Same journal

Enhancing Cross-Context Generalization in Drug Perturbation Prediction with a Multimodal Conditional Diffusion Framework.

Bioinformatics (Oxford, England)·2026
Same journal

Primer Design through Submodular Function Estimation.

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

Related Experiment Video

Updated: Jun 4, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

SHRiMP2: sensitive yet practical SHort Read Mapping.

Matei David1, Misko Dzamba, Dan Lister

  • 1Department of Computer Science, Princeton University, USA.

Bioinformatics (Oxford, England)
|February 1, 2011
PubMed
Summary
This summary is machine-generated.

The updated SHRiMP2 software significantly enhances short read mapping sensitivity and accuracy for DNA sequencing. This tool efficiently aligns paired reads from various sequencing platforms, utilizing multi-core processors for speed.

More Related Videos

RNA In situ Hybridization in Whole Mount Embryos and Cell Histology Adapted for Marine Elasmobranchs
08:13

RNA In situ Hybridization in Whole Mount Embryos and Cell Histology Adapted for Marine Elasmobranchs

Published on: April 12, 2013

Planarian Scrunching as a Quantitative Behavioral Readout for Noxious Stimuli Sensing
10:15

Planarian Scrunching as a Quantitative Behavioral Readout for Noxious Stimuli Sensing

Published on: July 30, 2020

Related Experiment Videos

Last Updated: Jun 4, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

RNA In situ Hybridization in Whole Mount Embryos and Cell Histology Adapted for Marine Elasmobranchs
08:13

RNA In situ Hybridization in Whole Mount Embryos and Cell Histology Adapted for Marine Elasmobranchs

Published on: April 12, 2013

Planarian Scrunching as a Quantitative Behavioral Readout for Noxious Stimuli Sensing
10:15

Planarian Scrunching as a Quantitative Behavioral Readout for Noxious Stimuli Sensing

Published on: July 30, 2020

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The original Short Read Mapping Program (SHRiMP) has undergone a major update to version 2.
  • Advancements in next-generation sequencing necessitate improved read mapping tools.

Purpose of the Study:

  • To introduce SHRiMP2, a significantly updated short read mapping program.
  • To enhance mapping sensitivity and accuracy for diverse sequencing reads.

Main Methods:

  • SHRiMP2 supports both letter and color space (AB/SOLiD) reads.
  • Direct alignment of paired reads is enabled.
  • Parallel computation is utilized to leverage multi-core architectures for increased speed.

Main Results:

  • SHRiMP2 achieves high mapping sensitivity and accuracy.
  • The program offers a reasonable processing speed.
  • Optimized for efficient utilization of computational resources.

Conclusions:

  • SHRiMP2 represents a substantial improvement over the original SHRiMP.
  • The software provides a powerful and efficient solution for short read mapping in genomic analyses.
  • Freely available executables and source code facilitate widespread adoption and use.