This GitHub repository 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.
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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 ]
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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, Slides ]
[doi:10.1007/11428848_119](https://dl.acm.org/doi/10.1007/11428848_119)
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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)
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Masoumi, B. (2005) Simultaneous Alignment and Structure Prediction for Three RNA Sequences. Master's thesis, School of Information Technology and Engineering, University of Ottawa.