genePI - Gene promoter identification system

Tool does not work at the moment due to security breach. It will be up as soon as possible.

Due to a web application vulnerability, this site was recently infiltrated by a scriptbot that was passing by. The services and applications on the server have therefore been taken down for security audit, and are now slowly coming back up again. We apologise for any inconvenience this may have caused.

genePI is a classification system based on internal DNA properties that does not use any promoter- specific motif data. For its development, a support vector machine classifier was trained and tested using feature vectors based on predicted DNA properties, nucleotide content, sequence complexity and repeat data. The tool has been designed for detection of promoter regions, and does not give exact positions of TSSs.

We currently provide genePI predictions on the ENCODE regions as .gff files. Download

If you wish to generate your own predictions, please read carefully the input instructions! The default region length is 600bp, longer regions are scanned in 200bp steps. genePI currently provides raw classifier values, which are either positive (promoter regions) or negative (non-promoter regions). For a higher specificity, a threshold >=0.4 is recommended! Read more about genePI.

INPUT instructions:

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genePI is written and supported by Petra Schwalie. You can obtain a copy of the software to run locally here (You will also need to install RepeatMasker and Gist!). For more information please contact the author!

Bioinformatics & Gene Regulation
Department of Cancer Research and Molecular Medicine
Norwegian University of Science and Technology
Trondheim, Norway