EGASP: the human ENCODE Genome Annotation Assessment Project

Table 3 Summary of programs used to determine predictions submitted for each EGASP category

Submission category	Program	Affiliation	Reference
1 (AUGUSTUS-any)	AUGUSTUS	Georg-August-Universität, Göttingen	[58]
2 (AUGUSTUS-abinit)
3 (AUGUSTUS-EST)
4 (AUGUSTUS-dual)
1	FGENESH++	Softberry Inc.	[56]
1	JIGSAW	The Institute for Genomic Research (TIGR)	[59]
1 (PAIRAGON-any)	PAIRAGON and NSCAN_EST	Washington University, Saint Louis (WUSTL)	[57]
3 (PAIRAGON+NSCAN_EST)
2	GENEMARK.hmm	Georgia Institute of Technology	[60]
2	GENEZILLA	TIGR	[81]
3	ACEVIEW	National Center for Biotechnology Information (NCBI)	[52]
3	ENSEMBL	The Wellcome Trust Sanger Institute (WTSI) and	[64]
		European Bioinformatics Institute (EBI)
3	EXOGEAN	Ecole Normale Superieure, Paris	[62]
3	EXONHUNTER	University of Waterloo	[63]
4	ACESCAN*	Salk Institute	[82]
4	DOGFISH-C	WTSI	[67]
4	NSCAN	WUSTL	[57]
4	SAGA	University of California at Berkeley	[66]
4	MARS	WUSTL - EBI	[65]
5	GENEID-U12	Institut Municipal d'Investigació	-
5	SGP2-U12	Mèdica, Barcelona
6	ASPIC^†	Università degli Studi di Milano	[83]
6 (AUGUSTUS-exon)	AUGUSTUS	Georg-August-Universität, Göttingen	[58]
6	CSTMINER^‡	Università degli Studi di Milano	[84]
6	DOGFISH-C-E^§	WTSI	[67]
6	SPIDA	EBI	[85]
6	UNCOVER^§	Duke University	[86]
1	CCDSGene	UCSC tracks [7]	[55]
1	KNOWNGene		[54]
1	REFSEQ (REFGene)		[4]
2	GENEID		[19]
2	GENSCAN		[18]
3	ACEMBLY		[52]
3	ECGene		[53]
3	ENSEMBL (ENSGene)		[6]
3	MGCGene		[5]
4	SGP2		[9]
4	TWINSCAN		[12,13]
-	CODING 20050607	GENCODE annotation	[33]
-	GENES 20050607

A complete listing of the number of features for each sequence obtained by each method is available at the Supplementary material web page [51]. *The ACESCAN group submitted results only for the training set and, therefore, has not been evaluated. ^†ASPIC only provided results for the training regions and, therefore, has not been evaluated. Moreover, ASPIC submitted only intron annotations and should be considered in category 6. ^‡CSTMINER predicts coding regions but does not provide strand information. ^§DOGFISH-C-E and UNCOVER predict only novel exons; this makes it difficult to compare these methods with the others in the same category.

ISSN: 1474-760X