Welcome to Geptop 3.0 Help Page

To enable Geptop 3.0 to function properly, you need to provide the whole genome nucleic acid sequence file (in .fasta or .fna format) of the bacteria you want to predict. Please note that it should be a nucleic acid sequence, not an amino acid sequence, which can be obtained from the National Center for Biotechnology Information (NCBI) or sequenced by yourself. Example formats can be found on the Predict page. Here is a file includes 500 genes from Escherichia coli strain K-12 substrain MG1655, and is intended for use as a test input on the Predict interface.

You can adjust the essentiality score threshold (from 0 to 1) to change the number of predicted drug target proteins in the final result. A higher threshold will result in fewer final predictions, while a lower threshold will result in more final predictions.The default threshold is 0.3.

You can choose between two different operating modes for Geptop 3.0 based on your needs: Normal and Fast. Generally, the prediction performance of the Normal mode is about 1% higher than the Fast mode. However, the Normal mode takes around an hour to run, while the Fast mode only requires ten minutes to produce results. The default mode is Normal.

Geptop is also available as a standalone python script to run in a Linux or Windows environment. The file is available at the Download.