Eponine models consist of a set of DNA weight matrices recognizing specific sequence motifs. Each of these is associated with a position distribution relative to the transcription start site. The model currently in use on this server is shown below:

Eponine model 2

Eponine has been tested by comparing the output with annotated mRNAs from human chromosome 22. From this work, we estimate that using the default threshold (0.999) it detects >50% of transcription start sites, with around 70% specificity. However, it does not always predict the direction of transcription correctly -- an effect which seems to be common among computational TSS finders.

You can submit sequences for analysis with Eponine using a web interface. Copies of the scanning software are also available to download.

Citation

• Computational detection and location of transcription start sites in mammalian genomic DNA.

  Down TA and Hubbard TJ

  Genome research 2002;12;3;458-61

  PUBMED: 11875034; DOI: 10.1101/gr.216102; PMC: 155284

Running the Eponine scanner application

Eponine is distributed as an executable JAR file. It should run on any machine with Java Runtime Environment version 1.2 or later installed.

To run the scanner, use the following command line:

java -jar eponine-scan.jar -seq  -threshold 0.999

   The sequence file must be in FASTA format.  If the file contains
   multiple sequences, all of them will be scanned.

   Any threshold value between 0.9 and 1.0 can be used.

NOTE: there is no need to unpack the JAR file to run the application.

Web interface

Downloads

• eponine-scan.jar (scanner application)
• eponine-tss2.xml (TSS model. This is included in the scanner application)

Older versions of the Netscape browser interpret all JAR files as Netscape update files, and will report an error if you click on the link above. To avoid this problem, hold down SHIFT while clicking on the link.