Skip to main content
construction release_alert
Scholars@Duke will be undergoing maintenance April 11-15. Some features may be unavailable during this time.
cancel

Genome annotation assessment in Drosophila melanogaster.

Publication ,  Journal Article
Reese, MG; Hartzell, G; Harris, NL; Ohler, U; Abril, JF; Lewis, SE
Published in: Genome Res
April 2000

Computational methods for automated genome annotation are critical to our community's ability to make full use of the large volume of genomic sequence being generated and released. To explore the accuracy of these automated feature prediction tools in the genomes of higher organisms, we evaluated their performance on a large, well-characterized sequence contig from the Adh region of Drosophila melanogaster. This experiment, known as the Genome Annotation Assessment Project (GASP), was launched in May 1999. Twelve groups, applying state-of-the-art tools, contributed predictions for features including gene structure, protein homologies, promoter sites, and repeat elements. We evaluated these predictions using two standards, one based on previously unreleased high-quality full-length cDNA sequences and a second based on the set of annotations generated as part of an in-depth study of the region by a group of Drosophila experts. Although these standard sets only approximate the unknown distribution of features in this region, we believe that when taken in context the results of an evaluation based on them are meaningful. The results were presented as a tutorial at the conference on Intelligent Systems in Molecular Biology (ISMB-99) in August 1999. Over 95% of the coding nucleotides in the region were correctly identified by the majority of the gene finders, and the correct intron/exon structures were predicted for >40% of the genes. Homology-based annotation techniques recognized and associated functions with almost half of the genes in the region; the remainder were only identified by the ab initio techniques. This experiment also presents the first assessment of promoter prediction techniques for a significant number of genes in a large contiguous region. We discovered that the promoter predictors' high false-positive rates make their predictions difficult to use. Integrating gene finding and cDNA/EST alignments with promoter predictions decreases the number of false-positive classifications but discovers less than one-third of the promoters in the region. We believe that by establishing standards for evaluating genomic annotations and by assessing the performance of existing automated genome annotation tools, this experiment establishes a baseline that contributes to the value of ongoing large-scale annotation projects and should guide further research in genome informatics.

Duke Scholars

Altmetric Attention Stats
Dimensions Citation Stats

Published In

Genome Res

DOI

ISSN

1088-9051

Publication Date

April 2000

Volume

10

Issue

4

Start / End Page

483 / 501

Location

United States

Related Subject Headings

  • Sequence Homology, Amino Acid
  • Promoter Regions, Genetic
  • Genome
  • Genes, Insect
  • Expressed Sequence Tags
  • Drosophila melanogaster
  • Databases, Factual
  • DNA, Complementary
  • Computational Biology
  • Bioinformatics
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Reese, M. G., Hartzell, G., Harris, N. L., Ohler, U., Abril, J. F., & Lewis, S. E. (2000). Genome annotation assessment in Drosophila melanogaster. Genome Res, 10(4), 483–501. https://doi.org/10.1101/gr.10.4.483
Reese, M. G., G. Hartzell, N. L. Harris, U. Ohler, J. F. Abril, and S. E. Lewis. “Genome annotation assessment in Drosophila melanogaster.Genome Res 10, no. 4 (April 2000): 483–501. https://doi.org/10.1101/gr.10.4.483.
Reese MG, Hartzell G, Harris NL, Ohler U, Abril JF, Lewis SE. Genome annotation assessment in Drosophila melanogaster. Genome Res. 2000 Apr;10(4):483–501.
Reese, M. G., et al. “Genome annotation assessment in Drosophila melanogaster.Genome Res, vol. 10, no. 4, Apr. 2000, pp. 483–501. Pubmed, doi:10.1101/gr.10.4.483.
Reese MG, Hartzell G, Harris NL, Ohler U, Abril JF, Lewis SE. Genome annotation assessment in Drosophila melanogaster. Genome Res. 2000 Apr;10(4):483–501.

Published In

Genome Res

DOI

ISSN

1088-9051

Publication Date

April 2000

Volume

10

Issue

4

Start / End Page

483 / 501

Location

United States

Related Subject Headings

  • Sequence Homology, Amino Acid
  • Promoter Regions, Genetic
  • Genome
  • Genes, Insect
  • Expressed Sequence Tags
  • Drosophila melanogaster
  • Databases, Factual
  • DNA, Complementary
  • Computational Biology
  • Bioinformatics