nGASP – the nematode genome annotation assessment project

BMC Bioinformatics

Table 1 Participating groups and submitted gene sets.

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Blasiar et al, Saint Louis, USA	GESECA (D. Blasiar, unpublished)	cat4:1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Liang et al, Cold Spring Harbor, USA	Gramene (Liang et al, unpublished)	cat3:2, cat4:1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

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.

ISSN: 1471-2105