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EDNA (Energy Based Multiple Sequence Alignment) is a multiple sequence alignment (MSA) program for aligning transcription factor binding site sequences (TFBSs). The novelty of this software is the scoring using a thermodynamically generated null hypothesis. The method is well suited for aligning sequences that are often not related. Alternative names: Energy Based Multiple Sequence Alignment, EDNA


Phylogeny; Sequence analysis; Nucleic acid sites, features and motifs; Nucleic acid structure analysis; Sequence sites, features and motifs OPERATION=Multiple sequence alignment


  • Operation: Multiple sequence alignment
  • Software interface: Command-line user interface
  • Language: Java
  • Operating system: Linux; Mac OS X
  • License: Not stated
  • Cost: Free
  • Version name: 1.3.1
  • Maturity: Stable
  • Credit: Darwin Trust of Edinburgh.
  • Contact: dov.stekel _at_
  • Collection: -


Salama RA, Stekel DJ "A non-independent energy-based multiple sequence alignment improves prediction of transcription factor binding sites." Bioinformatics. 2013 Nov 1;29(21):2699-704.
PMID: 23990411

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