Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Commentary
  • Published:

EGASP: collaboration through competition to find human genes

According to the most recent estimates, the number of human genes is possibly—but not certainly—between 20,000 and 25,000. To contribute strategies to reduce this uncertainty, several groups working on computational gene prediction met recently at the Welcome Trust Sanger Institute with the goal to test and compare predictive methods of genome annotation.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Measuring accuracy of gene prediction tools against expert annotations.
Figure 2: Sensitivity and specificity at the exon level of several predictions submitted to EGASP'05.


  1. Venter, J.C. et al. Science 291, 1304–1351 (2001).

    Article  CAS  Google Scholar 

  2. Lander, E.S. et al. Nature 409, 860–921 (2001).

    Article  CAS  Google Scholar 

  3. Rogers, J. Cold Spring Harb. Symp. Quant. Biol. 68, 1–11 (2003).

    Article  CAS  Google Scholar 

  4. International Human Genome Sequencing Consortium. Nature 431, 931–945 (2004).

  5. Brent, M.R. & Guigo, R. Curr. Opin. Struct. Biol. 14, 264–272 (2004).

    Article  CAS  Google Scholar 

  6. ENCODE Project Consortium. Science 306, 636–340 (2004).

  7. Ashurst, J.L. & Collins, J.E. Annu. Rev. Genomics Hum. Genet. 4, 69–88 (2003).

    Article  CAS  Google Scholar 

  8. Reese, M.G. et al. Genome Res. 10, 483–501 (2000).

    Article  CAS  Google Scholar 

  9. Bajic, V.B. Brief Bioinform. 1, 214228 (2000).

    Article  Google Scholar 

  10. Baldi, P., Brunak, S., Chauvin, Y., Andersen, C.A. & Nielsen, H. Bioinformatics 16, 412–424 (2000).

    Article  CAS  Google Scholar 

  11. Burset, M. & Guigo, R. Genomics 34, 353–367 (1996).

    Article  CAS  Google Scholar 

Download references


The GENCODE annotation is mostly the effort of A. Frankish, D. Swarbreck, J. Gilbert, J. Ashurst and T. Hubbard from the Havana team at the Wellcome Trust Sanger Institute; of C. Ucla, A. Reymond and S. Antonarakis from the Faculté de Médecine Université de Genève, and of F. Denoeud, J. Lagarde and R. Guigó from the Institut Municipal d'Investigació Mèdica (IMIM) in Barcelona. P. Flicek from the European Bioinformatics Insitute and J.F. Abril from the IMIM were responsible for computing most of the accuracy measures. J. Ashurst, E. Birney, P. Good, R. Guigó and T. Hubbard participated in the organizing committee. M. Ashburner, V.B. Bajic, T. Gingeras, S. Lewis and M. Reese were members of the advisory committee. The workshop was part of the ENCODE project that is funded by the US National Institutes of Health NHGRI.

Author information

Authors and Affiliations


Rights and permissions

Reprints and permissions

About this article

Cite this article

Guigó, R., Reese, M. EGASP: collaboration through competition to find human genes. Nat Methods 2, 575–577 (2005).

Download citation

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing