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Volume 7 Supplement 1

EGASP '05: ENCODE Genome Annotation Assessment Project


Edited by Roderic Guigó, Martin G Reese

  1. Content type: Review

    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...

    Authors: 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…

    Citation: Genome Biology 2006 7(Suppl 1):S2

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  2. Content type: Review

    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...

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

    Citation: Genome Biology 2006 7(Suppl 1):S3

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  3. Content type: Research

    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...

    Authors: 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

    Citation: Genome Biology 2006 7(Suppl 1):S4

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  4. Content type: Research

    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...

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

    Citation: Genome Biology 2006 7(Suppl 1):S5

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  5. Content type: Research

    Predicting complete protein-coding genes in human DNA remains a significant challenge. Though a number of promising approaches have been investigated, an ideal suite of tools has yet to emerge that can provide...

    Authors: Jonathan E Allen, William H Majoros, Mihaela Pertea and Steven L Salzberg

    Citation: Genome Biology 2006 7(Suppl 1):S9

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  6. Content type: Research

    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...

    Authors: Victor Solovyev, Peter Kosarev, Igor Seledsov and Denis Vorobyev

    Citation: Genome Biology 2006 7(Suppl 1):S10

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  7. Content type: Research

    A large number of gene prediction programs for the human genome exist. These annotation tools use a variety of methods and data sources. In the recent ENCODE genome annotation assessment project (EGASP), some ...

    Authors: Mario Stanke, Ana Tzvetkova and Burkhard Morgenstern

    Citation: Genome Biology 2006 7(Suppl 1):S11

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