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.

Guigó et al. Genome Biology 2006 7(Suppl 1):S2   doi:10.1186/gb-2006-7-s1-s2