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Table 1 Participating groups and submitted gene sets.

From: nGASP – the nematode genome annotation assessment project

Participating group Program name Number of gene sets submitted in each category
Blasiar et al, Saint Louis, USA GESECA (D. Blasiar, unpublished) cat4:1
Borodovsky et al, Atlanta, USA GeneMark.hmm [24] cat1:1
Brent et al, Saint Louis, USA N-SCAN [25] cat2:1
Durbin et al, Cambridge, UK GENOMIX [26] cat4:2
Guigó et al, Barcelona, Spain GeneID1 [27], SGP2 [28] GeneID: cat1:1, cat4:2; SGP2: cat2:1
Korf et al, Davis, USA SNAP [29] cat1:1
Krogh et al, Copenhagen, Denmark Agene [30] cat1:1
Liang et al, Cold Spring Harbor, USA Gramene (Liang et al, unpublished) cat3:2, cat4:1
Pereira et al, Pennsylvania, USA Evigan [31], CRAIG [32] CRAIG: cat1:1; Evigan: cat4:1
Rätsch et al, Tübingen, Germany MGENE (Schweikert et al, submitted) cat1:3, cat2:2, cat3:3
Roos et al, Pennsylvania, USA GLEAN [33] cat4:1
Salzberg et al, Maryland, USA JIGSAW [14], GlimmerHMM [14] GlimmerHMM: cat1:1; JIGSAW: cat4:2
Schiex et al, Toulouse, France EUGENE [34] cat1:1, cat2:1, cat3:2, cat4:4
Solovyev et al, University of London and Softberry Inc, New York, USA Fgenesh, Fgenesh++, Fgenesh++C [13] Fgenesh: cat1:1; Fgenesh++: cat3:1; Fgenesh++C: cat4:1
Stanke, Santa Cruz, USA AUGUSTUS [12] cat1:2, cat3:1
Brejová & Vinar, New York, USA ExonHunter [35] cat1:1, cat3:2
Yandell et al, Berkeley, USA MAKER (using SNAP) [36] cat3:2
  1. 1The GeneID gene set was submitted after the nGASP deadline. The research groups that participated in nGASP, the names of the software used to produce gene prediction sets, and the number of gene sets submitted in each of the nGASP categories by a research group, are given. There were four nGASP categories: category 1 predictions were made by ab initio gene-finders; category 2 predictions by gene-finders that use multi-genome alignments; category 3 predictions by gene-finders that take advantage of EST/mRNA or protein alignments; and category 4 predictions by gene prediction systems that use gene models created by other annotation software, and any of the data used as input for gene-finders in the other three categories. Here 'cat3:2' means that 2 gene sets in category 3 were submitted. In some cases a group submitted two gene sets produced by using different parameters of their software to the same nGASP category.
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