Eponine

[Genome Research Limited]

Eponine is a probabilistic method for detecting transcription start sites (TSS) in mammalian genomic sequence, with good specificity and excellent positional accuracy.

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 model 2

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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.

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

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 <sequence-file> -threshold <threshold-value>
sequence-file
The sequence file must be in FASTA format. If the file contains multiple sequences, all of them will be scanned.
threshold-value
Any threshold value between 0.9 and 1.0 can be used.

Notes

  • There is no need to unpack the JAR file to run the application.

Downloads

Notes

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* quick link - http://q.sanger.ac.uk/5xge7g4h