Description

Eponine is 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 transcription start site. The model currently in use on this server is shown below:

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.

Thomas A. Down and Tim J. P. Hubbard. 2002. Computational Detection and Location of Transcription Start Sites in Mammalian Genomic DNA Genome Res. 12:458-461.

Credits

Thanks to Thomas Down at the Sanger Institute for providing the Eponine program, which was run at UCSC to produce this track.