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Profile-Dynalign 1.0


This web site contains information about the software system Profile-Dynalign. We extended the program Dynalign (Mathews & Turner (2002) JMB 317(2):191-203 --- an algorithm for finding the secondary structure common to two RNA sequences) to align profiles of multiple sequences. We also explored the relative successes of different approaches to designing the tree that will guide progressive alignments of sequence profiles to create a multiple sequence alignment and prediction of conserved structure.


Profile-Dynalign is an extension of Dynalign, written by David Mathews. An initial prototype for the alignment of two profiles was developed by Luke Cen (Winter 2006). It was then further extended by Amelia Bellamy-Royds (Summer 2006) who wrote the source code and analysed the data for the various approches to designing guide trees. The work was done under the supervision of Marcel Turcotte.


The project is documented by the following publication.
  • A. Bellamy-Royds and M. Turcotte. (2007) Can clustal-style progressive pairwise alignment of multiple sequences be applied to RNA secondary structure prediction? BMC Bioinformatics, 8:190, 2007.



Download: profile-dynalign.tar.gz