General Information
| Description | Display and analysis of cis-regulatory modules |
| Homepage | http://labs.bio.unc.edu/crews/twine/ |
Publications
Twine: display and analysis of cis-regulatory modules
Summary:
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.
Availability:
Twine is freely available as a compiled Java .jar package or Java source code at http://labs.bio.unc.edu/crews/twine/.
Contact:
steve_crews@unc.edu
Supplementary information:
Supplementary data are available at Bioinformatics online.
Related Tools
coMOTIF
Published July 2011
A mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq Data
BLSSpeller
Published August 2015
Exhaustive comparative discovery of conserved cis-regulatory elements
EnhancerAtlas
Published August 2016
A resource for enhancer annotation and analysis in 105 human cell/tissue types
BiRen
Published February 2017
Predicting enhancers with a deep-learning-based model using the DNA sequence alone
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