Volume 7 Supplement 1

EGASP '05: ENCODE Genome Annotation Assessment Project


Edited by Roderic Guigó, Martin G Reese

  1. Review

    EGASP: the human ENCODE Genome Annotation Assessment Project

    We present the results of EGASP, a community experiment to assess the state-of-the-art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence. The experiment had two major g...

    Roderic Guigó, Paul Flicek, Josep F Abril, Alexandre Reymond, Julien Lagarde, France Denoeud, Stylianos Antonarakis, Michael Ashburner, Vladimir B Bajic, Ewan Birney, Robert Castelo, Eduardo Eyras, Catherine Ucla, Thomas R Gingeras, Jennifer Harrow, Tim Hubbard…

    Genome Biology 2006 7(Suppl 1):S2

    Published on: 7 August 2006

  2. Review

    Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment

    This study analyzes the predictions of a number of promoter predictors on the ENCODE regions of the human genome as part of the ENCODE Genome Annotation Assessment Project (EGASP). The systems analyzed operate...

    Vladimir B Bajic, Michael R Brent, Randall H Brown, Adam Frankish, Jennifer Harrow, Uwe Ohler, Victor V Solovyev and Sin Lam Tan

    Genome Biology 2006 7(Suppl 1):S3

    Published on: 7 August 2006

  3. Research

    GENCODE: producing a reference annotation for ENCODE

    The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual annotation by the HAVANA team, experimental valida...

    Jennifer Harrow, France Denoeud, Adam Frankish, Alexandre Reymond, Chao-Kung Chen, Jacqueline Chrast, Julien Lagarde, James GR Gilbert, Roy Storey, David Swarbreck, Colette Rossier, Catherine Ucla, Tim Hubbard, Stylianos E Antonarakis and Roderic Guigo

    Genome Biology 2006 7(Suppl 1):S4

    Published on: 7 August 2006

  4. Research

    Pairagon+N-SCAN_EST: a model-based gene annotation pipeline

    This paper describes Pairagon+N-SCAN_EST, a gene annotation pipeline that uses only native alignments. For each expressed sequence it chooses the best genomic alignment. Systems like ENSEMBL and ExoGean rely on t...

    Manimozhiyan Arumugam, Chaochun Wei, Randall H Brown and Michael R Brent

    Genome Biology 2006 7(Suppl 1):S5

    Published on: 7 August 2006

  5. Research

    Automatic annotation of eukaryotic genes, pseudogenes and promoters

    The ENCODE gene prediction workshop (EGASP) has been organized to evaluate how well state-of-the-art automatic gene finding methods are able to reproduce the manual and experimental gene annotation of the huma...

    Victor Solovyev, Peter Kosarev, Igor Seledsov and Denis Vorobyev

    Genome Biology 2006 7(Suppl 1):S10

    Published on: 7 August 2006

  6. Research

    AceView: a comprehensive cDNA-supported gene and transcripts annotation

    Regions covering one percent of the genome, selected by ENCODE for extensive analysis, were annotated by the HAVANA/Gencode group with high quality transcripts, thus defining a benchmark. The ENCODE Genome Ann...

    Danielle Thierry-Mieg and Jean Thierry-Mieg

    Genome Biology 2006 7(Suppl 1):S12

    Published on: 7 August 2006