This is 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.
Amelia B. Bellamy-Royds and Marcel Turcotte (Submitted) Can Clustal-Style Progressive Pairwise Alignment of Multiple Sequences Be Used in RNA Secondary Structure Prediction?
PREREQUISITE: emma from EMBOSS is required for building tree from sequence information.
In order to build the main program, go to the source code directory (src), edit the make file to suite your needs and type make. Copy the executable (pdynalign) to a directory specified by the environment PATH.
DYNALIGN_DIR should be pointing at the directory that contains the energy tables (datafiles).
PERLLIB should be pointing at the scripts directory.
[ Main scripts ]
allpairs.prl:
Creates a set of all pairwise Profile-Dynalign alignments.
bestprog.prl:
Creates a Profile-dynalign alignment in a progressive fashion by
joining sequences with the best energy scores from all pairwise
alignments (requires running allpairs.prl first).
besttree.prl:
Creates a Profile-dynalign alignment using a nearest-neighbour
tree based on the energy scores from all pairwise alignments
(requires running allpairs.prl first).
clustalwtree.prl:
Creates a Profle-dynalign alignment using a phylogenetic tree
structure determined from a Clustal W primary sequence alignment.
randbaltree.prl:
Creates a Profile-Dynalign alignment using a randomized balanced
tree structure.
randprogtree.prl:
Creates a Profile-Dynalign alignment by progressively adding one
sequence in random order.
[ Utilities ]
seq2prf.prl:
Converts a Dynalign-style .seq file into Stockholm profile .prf
format.
ct2mfoldaux.prl:
Extracts a set of constraints for mfold from a connect (ct) file.
bracket2ct:
Converts a file in bracket notation to ct format.
ct_compare:
Compares two ct files (a reference and a predction) so as to
produce statistics: ppv, coverage and MCC.
The directory examples contains sample scripts for each of the five approaches for building the guide trees, as well as computing all the pairwise alignments.
Marcel Turcotte [email protected]