Table 3 |
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|
Summary of programs used to determine predictions submitted for each EGASP category |
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|
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 |
||
|
|
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|
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. |
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|
Guigó et al. Genome Biology 2006 7(Suppl 1):S2 doi:10.1186/gb-2006-7-s1-s2 |
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