Orphelia [Results]

Results

The performance of Orphelia with the models Net300 and Net700 was evaluated on randomly excised DNA fragments of 300 bp and 700 bp length. The fragments were sampled to 10-fold genome coverage from the species Archeaoglobus fulgidus, Methanococcus jannaschii, Natronomonas pharaonis, Buchnera aphidicola, Bacillus subtilis, Corynebacterium jeikeium, Chlorobium tepidum, Escherichia coli, Helicobacter pylori, Prochlorococcus marinus, and Wolbachia endosymbiont. Mean and standard deviation were calculated over all species.

Sensitivity reflects how many of the annotated genes were detected by a gene finder, while specificity shows how many of the predictions are correct.

For comparison, we show the performance of GeneMark [1], MetaGene [2], and the MetaGeneAnnotator [3]:

ToolSens. (300 bp)Spec. (300 bp)Sens. (700 bp)Spec. (700 bp)
Orphelia Net30082.1 +/- 3.691.7 +/- 13.8
Orphelia Net70088.4 +/- 3.192.9 +/- 3.2
MetaGene89.3 +/- 3.384.2 +/- 6.092.6 +/- 3.188.6 +/- 5.9
MetaGeneAnnotator90.1 +/- 2.886.2 +/- 5.792.9 +/- 3.090.0 +/- 6.0
GeneMark87.4 +/- 2.891.0 +/- 4.290.9 +/- 2.792.2 +/- 5.1

Predictions of Orphelia (Net700) and MetaGene on hypersaline microbial mat metagenome [4]



[1] Besemer J. and Borodovsky M., Heuristic approach to deriving models for gene finding, NAR, 1999, Vol. 27, No. 19, pp. 3911-3920.
[2] Noguchi H., Park J., Takagi T., MetaGene: prokaryotic gene finding from environmental genome shotgun sequencies, NAR, 2006, Vol. 34, No. 19, pp. 5623-5630.
[3] Noguchi H., Taniguchi T., Itoh T., MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage genomes, DNA Res., 2008, Vol. 15, No. 6, pp. 387-396.
[4] Kunin V., Raes J., Harris J.K., Spear J.R., Walker J.J., Ivanova N., von Mering C., Bebout B.M., Pace N.R., Bork P., Hugenholtz P.. Millimeterscale genetic gradients and community level molecular convergence in a hypersaline microbial mat. Molecular Systems Biol., 4:198, 2008.


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