eXtended Dynalign 1.0
INTRODUCTION
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.HISTORY
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.PUBLICATIONS
The project is documented by the following publications.- 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 ] - 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 ] doi:10.1007/11428848_119 - 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 ] - Masoumi, B. (2005) Simultaneous Alignment and Structure Prediction for Three RNA Sequences. Master's thesis, School of Information Technology and Engineering, University of Ottawa.