msa-edna

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

Topic

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

Detail

  • Operation: Multiple sequence alignment

  • Software interface: Command-line user interface

  • Language: Java

  • License: -

  • Cost: Free

  • Version name: 1.3.1

  • Credit: Darwin Trust of Edinburgh.

  • Input: -

  • Output: -

  • Contact: dov.stekel@nottingham.ac.uk

  • Collection: -

  • Maturity: Stable

Publications

  • A non-independent energy-based multiple sequence alignment improves prediction of transcription factor binding sites.
  • Salama RA and Stekel DJ. A non-independent energy-based multiple sequence alignment improves prediction of transcription factor binding sites. A non-independent energy-based multiple sequence alignment improves prediction of transcription factor binding sites. 2013; 29:2699-704. doi: 10.1093/bioinformatics/btt463
  • https://doi.org/10.1093/bioinformatics/btt463
  • PMID: 23990411
  • PMC: -

Download and documentation

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