## Description

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

## Methods

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 TSS.

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 approximately 70% specificity. However, it does not always predict the direction of transcription correctly—an effect that seems to be common among computational TSS finders.

## Credits

Thanks to Thomas Down at the Sanger Institute for providing the Eponine program (version 2, March 6, 2002) which was run at UCSC to produce this track.

## References

Down TA, Hubbard TJP. Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res. 2002 Mar;12(3):458-61.