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

Vertebrate gene finding from multiple-species alignments using a two-level strategy.

David Carter1, Richard Durbin

  • 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. dmc@sanger.ac.uk

Genome Biology
|August 24, 2006
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

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

bioRxiv : the preprint server for biology·2026
Same author

Maternal Thyroid Supplementation Prevents Autistic-relevant Social Behavior and Hypothalamic Oxytocin Depletion Produced by Developmental Exposure to Environmental Toxicants.

bioRxiv : the preprint server for biology·2026
Same author

A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.

bioRxiv : the preprint server for biology·2026
Same author

Cryptic Diversity and Impacts of Domestication in the Black Soldier Fly (Hermetia illucens) Genome.

Genome biology and evolution·2026
Same author

Pangenome-guided sequence assembly via binary optimization.

Briefings in bioinformatics·2026
Same author

The Genomics of Convergent Adaptation to Intertidal Gravel Beaches in Mediterranean Clingfishes.

Genome biology and evolution·2026
Same journal

Defined bacterial consortium highlights the impact of intestinal bacteria on DNA methylation and tumorigenesis.

Genome biology·2026
Same journal

Somatic mobility of transposons is explosive and shaped by distinct integration biases in Arabidopsis thaliana.

Genome biology·2026
Same journal

UK Biobank whole-genome sequencing reveals robust contributions of rare variants to complex-trait heritability.

Genome biology·2026
Same journal

A one-week automated genome-wide optical pooled screen using OttoSeq.

Genome biology·2026
Same journal

Integrated lipidomic and transcriptomic profiling of the host response in human malaria.

Genome biology·2026
Same journal

Centromeric satellite expansion drives genome evolution in the snowy owl.

Genome biology·2026
See all related articles

DOGFISH improves gene structure prediction in vertebrates by analyzing multiple species alignments. This method identifies over 10,000 new coding exons in the human genome, aiding experimental verification.

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Gene structure prediction accuracy in vertebrates can be enhanced through comparative genomics.
  • Conserved functional regions across related species improve prediction reliability.

Purpose of the Study:

  • To develop and present DOGFISH, a novel vertebrate gene finder.
  • To improve the accuracy of gene structure prediction using multiple species alignments.

Main Methods:

  • DOGFISH employs a separated site classifier and structure predictor.
  • The classifier scores splice sites using multi-species alignments.
  • The predictor hypothesizes coding transcripts and identifies novel exons.

Main Results:

Related Experiment Videos

  • DOGFISH performance was assessed on ENCODE regions.
  • Transcripts and exons were predicted across the human genome.
  • Over 10,000 high-confidence novel coding exons were identified, not present in the Ensembl gene set.

Conclusions:

  • DOGFISH offers a practical multi-species gene prediction method.
  • Prediction accuracy increases with the number of species analyzed (up to at least eight).
  • Novel predictions from the whole-genome scan facilitate experimental validation.