Geptop

Essential genes are absolutely required for the survival of an organism and are therefore considered the foundation of life. For effectively predicting essential genes, we formed an online and also a standalone tool designated as Geptop (http://cefg.uestc.edu.cn/geptop/).

After a user submits the whole-proteome for a bacterial species in the FASTA format, the web server will automatically compute the essentiality score for each gene by comparing the orthology and phylogeny information for the 19 genome datasets (from DEG). The default cutoff is set at 0.15. The result will be automatically sent to the user via e-mail when the prediction is completed. Alternatively, a standalone version Geptop is also available. This package is dependent on Python, Biopython and BLAST+.

In a series of tests, our Geptop method yielded higher area under curve (AUC) scores in the receiver operating curves than the integrative approaches. In the ten-fold cross-validations among randomly upset samples, Geptop yielded an AUC of 0.918, and in the cross-organism predictions for 19 organisms Geptop yielded AUC scores between 0.569 and 0.959.

Citation: Wei W, Ning L-W, Ye Y-N, Guo F-B (2013) Geptop: A Gene Essentiality Prediction Tool for Sequenced Bacterial Genomes Based on Orthology and Phylogeny. PLoS ONE 8(8): e72343. doi:10.1371/journal.pone.0072343