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 Videos

CAP3: A DNA sequence assembly program.

X Huang1, A Madan

  • 1Department of Computer Science, Michigan Technological University, Houghton, Michigan 49931 USA. huang@mtu.edu

Genome Research
|October 6, 1999
PubMed
Summary
This summary is machine-generated.

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

TB yields from expanded contact tracing investigations.

Public health action·2025
Same author

Evaluation of treatment outcomes and associated risk factors in children with TB in Bangladesh.

Public health action·2025
Same author

The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness.

Journal of affective disorders·2020
Same author

Usability of daily SF36 questionnaires to capture the QALD variation experienced after vaccination with AS03<sub>A</sub>-adjuvanted monovalent influenza A (H5N1) vaccine in a safety and tolerability study.

Health and quality of life outcomes·2019
Same author

Insula and amygdala resting-state functional connectivity differentiate bipolar from unipolar depression.

Acta psychiatrica Scandinavica·2017
Same author

Unusual Presentation of Necrotic Erythema Nodosum Leprosum on Scalp: A Case Report.

Indian journal of leprosy·2015
Same journal

Complete sequencing of medaka genomes reveals the architecture of centromeric satellites, giant mobile elements, and sex chromosomes.

Genome research·2026
Same journal

Convergence and conflict among telomere specialized transposons across 60 million years of Drosophilid evolution.

Genome research·2026
Same journal

A unified analysis of cell type- and trajectory-associated pathways in single-cell data using Phoenix.

Genome research·2026
Same journal

Resf1 is required for proper placental development and configuration of trophoblast cell-specific heterochromatin.

Genome research·2026
Same journal

Telomere-driven replicative crisis is driven by large-scale changes in genomic architecture.

Genome research·2026
Same journal

Spatially informed reference-free cell-type deconvolution for spatial transcriptomics with SpatialCD.

Genome research·2026
See all related articles

The CAP3 program, a DNA sequence assembly tool, now offers improved quality clipping and error correction. It provides fewer consensus errors than PHRAP, aiding in scaffold construction.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • High-throughput sequencing generates vast amounts of DNA reads requiring efficient assembly.
  • Accurate sequence assembly is crucial for genome mapping and analysis.
  • Existing assembly programs have limitations in handling low-quality data and complex genomic structures.

Purpose of the Study:

  • To introduce the third generation of the CAP sequence assembly program (CAP3).
  • To highlight new features and improvements in CAP3 for enhanced DNA sequence assembly.
  • To evaluate CAP3's performance against established assemblers like PHRAP.

Main Methods:

  • CAP3 incorporates quality clipping for 5' and 3' read ends.
  • Utilizes base quality values for overlap computation, multiple sequence alignment, and consensus generation.

Related Experiment Videos

  • Employs forward-reverse constraints to correct assembly errors and link contigs.

    • Main Results:

    • CAP3 demonstrates effective quality clipping and error correction using base quality values.
    • Comparison with PHRAP shows CAP3 yields fewer errors in consensus sequences.
    • CAP3 facilitates easier scaffold construction, particularly with low-pass data and forward-reverse constraints.

    Conclusions:

    • The enhanced CAP3 program offers significant improvements for DNA sequence assembly.
    • CAP3 provides a valuable alternative to PHRAP, especially when consensus accuracy and scaffold construction are prioritized.
    • The integration of quality values and constraints enhances the reliability of genome assembly.