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

Increasing consensus accuracy in DNA fragment assemblies by incorporating fluorescent trace representations

C F Allex1, S F Baldwin, J W Shavlik

  • 1Computer Sciences Department, University of Wisconsin-Madison 53706, USA. allex@cs.wisc.edu

Proceedings. International Conference on Intelligent Systems for Molecular Biology
|January 1, 1997
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

Biomedical informatics training at the University of Wisconsin-Madison.

Yearbook of medical informatics·2007
Same author

Sex-specific SCAR markers in the dioecious plant Rumex nivalis (Polygonaceae) and implications for the evolution of sex chromosomes.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·2003
Same author

Storage and mobilization as antagonistic functional constraints on seed storage globulin evolution.

Journal of experimental botany·2003
Same author

Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T.

Infection and immunity·2003
Same author

Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli.

Proceedings of the National Academy of Sciences of the United States of America·2002
Same author

Nunatak survival of the high Alpine plant Eritrichium nanum (L.) Gaudin in the central Alps during the ice ages.

Molecular ecology·2002

A new Trace-Evidence method improves DNA sequence assembly accuracy by directly using aligned trace data. This approach yields more precise consensus sequences with less data coverage compared to traditional methods.

Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • DNA sequencing generates large datasets requiring accurate assembly.
  • Current consensus methods often struggle with ambiguity and require high data coverage.

Purpose of the Study:

  • To introduce and evaluate the Trace-Evidence method for DNA sequence assembly.
  • To demonstrate improved accuracy and reduced coverage requirements compared to existing methods.

Main Methods:

  • Developed the Trace-Evidence method incorporating aligned ABI trace information.
  • Utilized a novel representation, Trace-Data Classifications, for evidence extraction.
  • Calculated consensus calls by summing evidence from the representation.

Main Results:

Related Experiment Videos

  • Trace-Evidence produced more accurate and less ambiguous consensus sequences.
  • The method achieved low error rates with significantly less coverage (e.g., coverage of three).
  • Error rates with Trace-Evidence and low coverage rivaled standard methods using over ten-fold coverage.

Conclusions:

  • Trace-Evidence offers a superior approach to DNA sequence assembly.
  • The method enhances accuracy and efficiency in consensus sequence determination.
  • Reduced coverage requirements make Trace-Evidence a valuable tool for genomic research.