Introduction

Many algorithms analyze enhancers for overrepresentation of known and novel motifs, with the goal of identifying binding sites for direct regulators of gene expression. Twine is a Java GUI with multiple graphical representations ('Views') of enhancer alignments that displays motifs, as IUPAC consensus sequences or position frequency matrices, in the context of phylogenetic conservation to facilitate cis-regulatory element discovery. Thresholds of phylogenetic conservation and motif stringency can be altered dynamically to facilitate detailed analysis of enhancer architecture. Views can be exported to vector graphics programs to generate high-quality figures for publication. Twine can be extended via Java plugins to manipulate alignments and analyze sequences.Twine is freely available as a compiled Java .jar package or Java source code at http://labs.bio.unc.edu/crews/twine/.Supplementary data are available at Bioinformatics online.

Publications

  1. Twine: display and analysis of cis-regulatory modules.
    Cite this
    Pearson JC, Crews ST, 2013-07-01 - Bioinformatics (Oxford, England)

Credits

  1. Joseph C Pearson
    Developer

    Department of Biochemistry and Biophysics and Program in Molecular Biology and Biotechnology, The University of North Carolina at Chapel Hill, United States of America

  2. Stephen T Crews
    Investigator

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Summary
AccessionBT006621
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByStephen T Crews