Initiation code datasets

This directory contains information related to the manuscript "A code for trancriptional initiation in mammalian genomes" by frith MC et al.


2008-02-05: Added more explanatory comments in

2008-02-05: Web address changed to

Perl scripts

The scripts begin with comments explaining how to use them.

TSS clusters

Sequences used to find overrepresented DNA motifs and train PSMMs

PSMMs were derived from the central regions of these sequences, excluding sequences from chromosome 1.

Test sequences for PSMMs

The PSMMs were tested on the DNA sequences of TSS clusters <= 100 bp with stability >=2 in hg17 chromosome 1. Just enough flanking sequence was added to scan with PSMMs of +-50 regions.

Observed TSS usage in test sequences

(Excluding flanking sequence)

Position-specific Markov models

PSMM predictions