The structure of the HMM with <i>n</i> transcription factors (TFs).

<p>It is composed of <i>n</i> TF blocks and two background states. Between TF blocks and a background block is a branch. Each PSSM block is labeled with an alphabet. Background states are labeled with ‘x’. To model a forward and reverse PSSM, a PSSM block has 2<i>s</i>+2 states inside, where <i>s</i> is the length of a PSSM.</p

ROC curves for the cis-module predication.

<p>The prediction performance of COMET <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005501#pone.0005501-Frith2" target="_blank">[10]</a>, Cluster-Buster <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005501#pone.0005501-Frith3" target="_blank">[11]</a>, Stubb <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005501#pone.0005501-Sinha1" target="_blank">[15]</a> and the proposed HMM approach are compared.</p

Dataset of 4 TFs.

<p>Dataset of 4 TFs.</p

Assigned value on each label based on the ChIP-chip ratio.

<p>Assigned value on each label based on the ChIP-chip ratio.</p

Binding motifs for the four TFs used in establishing the CRM.

<p>The sequence logos were generated using WebLogo <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005501#pone.0005501-Crooks1" target="_blank">[30]</a>.</p

Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides-0

<p><b>Copyright information:</b></p><p>Taken from "Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides"</p><p>Nucleic Acids Research 2006;34(3):1082-1082.</p><p>Published online 13 Feb 2006</p><p>PMCID:PMC1369284.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p