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.