EP3 1.10 – Promoter Prediction Program

EP3 1.10

:: DESCRIPTION

EP3 (Easy Promoter Prediction Program) is a tool for the identification of the core region of a eukaryotic gene promoter. It uses universal properties of the promoter to detect those regions in a whole genome context. EP3 has been tested on several eukaryotes ranging from protists to human. On human it is, at the moment, the best performing tool to identify regions that are associated with transcription initiation.

::DEVELOPER

Van de Peer Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Java

:: DOWNLOAD

 EP3

:: MORE INFORMATION

Citation:

Abeel, T., Saeys, Y., Bonnet, E., Rouz?, P., Van de Peer, Y. (2008)
Generic eukaryotic core promoter prediction using structural features of DNA.
Genome Research 18, 310-23.

pppbenchmark 1.3 – Promoter Prediction Programs

pppbenchmark 1.3

:: DESCRIPTION

pppbenchmarkis a large-scale benchmarking study of 17 state-of-the-art PPPs (Promoter Prediction Programs). A multi-faceted evaluation strategy is proposed that can be used as a gold standard for promoter prediction evaluation, allowing authors of promoter prediction software to compare their method to existing methods in a proper way. This evaluation strategy is subsequently used to compare the chosen promoter predictors, and an in-depth analysis on predictive performance, promoter class specificity, overlap between predictors and positional bias of the predictions is conducted.

:DEVELOPER

Van de Peer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  pppbenchmark 

:: MORE INFORMATION

Citation:

Abeel, T., Van de Peer, Y., Saeys, Y. (2009)
Towards a gold standard for promoter prediction evaluation.
Bioinformatics 25, i313-i320.

ProSOM 2.5 – Promoter Prediction Program

ProSOM 2.5

:: DESCRIPTION

ProSOM is a promoter prediction program based on unsupervised clustering of physical properties of DNA. The program can clearly distinguish between the structural profiles of promoter sequences and other genomic sequences by using self-organizing maps.

:DEVELOPER

Van de Peer Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  ProSOM

:: MORE INFORMATION

Citation:

Abeel, T., Saeys, Y., Rouzé, P., Van de Peer, Y. (2008)
ProSOM: Core promoter prediction based on unsupervised clustering of DNA physical profiles.
Bioinformatics 24, i24-i31.