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eXtended Dynalign 1.0


This web site contains information about the software system eXtended Dynalign (X-Dynalign for short). This program takes as input three RNA sequences and produces a three-way sequence alignment, as well as a common secondary structure. The objective function consists of a linear combination of the free-energy of each sequence, given the common secondary structure, and an empirical term for gap penalties.


X-Dynalign is a direct extension of Dynalign, written by David Mathews. X-Dynalign was developed at the University of Ottawa by Beeta Masoumi under the supervision of Marcel Turcotte.


The project is documented by the following publications.
  1. Masoumi, B. and Turcotte, M. (2005) Simultaneous alignment and structure prediction of three RNA sequences. Int. J. Bioinformatics Research and Applications. Vol. 1, No. 2, pp. 230-245
    [ Paper ]

  2. Beeta Masoumi and Marcel Turcotte. Simultaneous alignment and structure prediction of RNAs: Are three input sequences better than two? In S. V. Sunderam et al., editor, 2005 International Conference on Computational Science (ICCS 2005), Lecture Notes in Computer Science 3515, pages 936-943, Atlanta, USA, May 22-25 2005.
    [ Paper | Web Appendix, PDF, PS | Slides ]


  3. Masoumi, B. and Turcotte, M. (2004) A Dynamic Programming Algorithm for Simultaneous Alignment and Structure Prediction of 3 RNA Sequences. BioNorth 2004 -- 11th Annual International Life Sciences and Biotechnology Conference and Exhibition. Ottawa, November 29 - December 1. (Poster)
    [ Abstract ]

  4. Masoumi, B. (2005) Simultaneous Alignment and Structure Prediction for Three RNA Sequences. Master's thesis, School of Information Technology and Engineering, University of Ottawa.


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