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

A gene-specific DNA sequencing chip for exploring molecular evolutionary change.

Olivier Fedrigo1, Gavin Naylor

  • 1Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA.

Nucleic Acids Research
|February 20, 2004
PubMed
Summary

This study introduces a novel gene-specific DNA chip design for DNA sequencing by hybridization (SBH). The approach efficiently identifies essential oligonucleotide probes, enabling accurate sequencing of target DNA with high coverage.

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 Vertebrate Genomes Project Phase I: A global reference genome resource.

bioRxiv : the preprint server for biology·2026
Same author

Assessing Climate Adaptation Among Canada Lynx (Lynx canadensis) Populations at the Trailing Edge.

Molecular ecology·2026
Same author

Long-Term Rock Dove (Columba livia) Primordial Germ Cell Culture: A Tool Towards Avian Conservation.

The Journal of heredity·2026
Same author

Reference genome assembly of the false killer whale (Pseudorca crassidens).

The Journal of heredity·2026
Same author

The reference genome of the Asian Elephant (Elephas maximus): a foundation for conservation and genomic research.

BMC genomics·2026
Same author

Genomic comparisons and the adaptive basis of brain size plasticity and chromosomal instability in the Eurasian common shrew.

Molecular biology and evolution·2026

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Sequencing by hybridization (SBH) faces challenges with probe length and the vast number of possible oligonucleotides.
  • Current DNA chip technology limits the inclusion of all necessary probes for reliable DNA binding and sequencing.

Purpose of the Study:

  • To develop a novel gene-specific DNA chip design to overcome limitations in SBH.
  • To identify a minimal set of oligonucleotide probes for efficient and accurate DNA sequencing.

Main Methods:

  • Utilized a training set of aligned gene sequences to identify essential oligonucleotide probes.
  • Employed a graph search algorithm to compute the minimum number of probes (15-30 bp) for capturing sequence variation.
  • Performed in silico testing using cytochrome-b sequences.

Related Experiment Videos

Main Results:

  • The novel approach significantly reduces the number of required oligonucleotide probes on a DNA chip.
  • Achieved an average of 98% sequence determination for unknown target DNA.
  • Demonstrated the feasibility of gene-specific probe selection for SBH.

Conclusions:

  • The proposed gene-specific DNA chip design effectively addresses the conflicting constraints in SBH.
  • This method offers a more efficient and technologically feasible approach to DNA sequencing using hybridization techniques.