title: Twine: display and analysis of cis-regulatory modules.
abstract: 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.
  
  
  BACKGROUND
  Twine is freely available as a compiled Java .jar package or Java source code at http://labs.bio.unc.edu/crews/twine/.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Department of Biochemistry and Biophysics and Program in Molecular Biology and Biotechnology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.
authors: Joseph C
authors: JC
authors: Pearson
authors: Stephen T
authors: ST
authors: Crews
mesh_terms: D000818:Animals; D001665:Binding Sites; D003196:Computer Graphics; D004742:Enhancer Elements, Genetic; D059372:Nucleotide Motifs; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors
references: Nat Rev Genet. 2011 Apr;12(4):283-93
references: 21358745
references: Pac Symp Biocomput. 2001;:127-38
references: 11262934
references: Bioinformatics. 2007 Apr 15;23(8):1032-4
references: 17308342
references: Bioinformatics. 2009 Oct 15;25(20):2730-1
references: 19654113
references: Development. 2004 May;131(10):2387-94
references: 15128669
references: Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):763-8
references: 11752406
references: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W86-91
references: 21715389
references: BMC Bioinformatics. 2007 Nov 01;8 Suppl 7:S21
references: 18047721
references: Genome Res. 2002 Jun;12(6):996-1006
references: 12045153
references: BMC Biol. 2010 Apr 21;8:49
references: 20409324
references: Dev Biol. 2004 Jul 15;271(2):431-8
references: 15223345
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D111-7
references: 21097781
references: Genome Res. 2002 Oct;12(10):1599-610
references: 12368253
references: Nucleic Acids Res. 2003 Jan 1;31(1):374-8
references: 12520026
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D105-10
references: 19906716