Predicted Gene counts in Drosophila genomes, 2006-08

See also Table of Gene Predictions Compared for sensitivity to old and new genes, and specificity to genes with evidence.

Key: (Source of Gene prediction data sets)
DGIL_SNO: SNAP predictor using homology evidence
RGUI_GID: geneid predictor
NCBI_GNO: GNOMON predictor using homology evidence
BREN_NSC: N-SCAN predictor using homology evidence
EISE_CGW: GeneWise (Dmel gene mapping)
BATZ_CNA: CONTRAST predictor
PACH_GMP: GeneMapper (Dmel gene mapping)
OXFD_GPI: Oxford gene pipeline (exonerate with Dmel gene mapping)
EISE_GLN: Glean prediction combiner
EISE_GLR: Glean prediction combiner, Dmel gene focus
UMD_JIG: Jigsaw prediction combiner

Don Gilbert, August 2006

Table 2. Drosophila species genome annotations (partial list) included at DroSpeGe, contributed at http://rana.lbl.gov/drosophila/wiki/index.php/Annotation_Submission

Contributor	Annotation Description
S. Batzoglou Lab, Stanford	BATZ_CNA: CONTRAST (6) predictions
M. Brent Lab, Washington Univ., St. Louis	BREN_NSC: N-SCAN (7) predictions with melanogaster alignments
D. Gilbert Lab, Indiana University	DGIL_SNO: SNAP (8) predictions, model organism gene homologies
M. Eisen Lab, UC Berkeley/LBNL	EISE_CGW: GeneWise (9), EISE_CGM: GeneMapper (10), EISE_CEX: Exonerate (11) annotations
R. Guigó Genome Bioinformatics Lab, Barcelona	GUI_GID: Geneid (12) predictions
J. Ostell lab, NCBI, Bethesda	NCBI_GNO: Gnomon (13) predictions
B. Oliver Lab, LCDB, NIDDK, NIH	OLIV_EXP: Gene expression evidence from microarray (14)
L. Pachter Lab, UC Berkeley	PACH_GMP: GeneMapper (10) annotations
C. Ponting Lab, MRC FGU Oxford	OXFD_GPI: Gene prediction pipeline (15) with Exonerate

References

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• 8. Korf, Ian 2004. Gene finding in novel genomes. BMC Bioinformatics 2004, 5:59 URL: http://www.biomedcentral.com/1471-2105/5/59
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• 11. Slater, G. St. C. and Ewan Birney, E. (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 2005, 6:31 doi:10.1186/1471-2105-6-31
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• 13. Souvorov, A., Hlavina, W., Kapustin, Y., Kiryutin, B., Kitts, P., Pruitt, K., Sapojnikov, V. and Ostell, J. (2006) Gnomon annotation of Drosophila species genomes. URL: ftp://ftp.ncbi.nih.gov/genomes/Drosophila_melanogaster/special_requests/CAF1/
• 14. Sturgill, D., Zhang, Y., Parisi, M., and Oliver, B. (2006) Drosophila species expression arrays, preliminary results. Laboratory of Cellular and Developmental Biology, NIDDK, NIH. URL: http://intramural.niddk.nih.gov/research/nimble/nimblefly.htm
• 15. Heger, A. and Ponting, C. (2006) Drosophila gene prediction pipeline with Exonerate. URL: http://wwwfgu.anat.ox.ac.uk:8080/flies/documentation.html