The Eponine program provides 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 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.
Thanks to Thomas Down at the
for providing the
Eponine program (version 2, March 6, 2002) which was run
at UCSC to produce this track.
Down TA, Hubbard TJP.
Computational detection and location of transcription start sites
in mammalian genomic DNA.
Genome Res. 2002 Mar;12(3):458-61.