RNAstructure Help
dynalign

dynalign is used to find the lowest free energy common secondary structures for two homologous sequences. It comes in two variants, dynalign and dynalign-smp. dynalign runs structure determination on a single processor, while dynalign-smp runs in parallel on a shared memory machine.

Required parameters:

Options which don't require added values:

NONE

Options which require added values:

NONE

Config file format:

The following example is based on sample.conf, a standard example found in the dynalign directory of the RNAstructure repository.

################################################################
# Required input
################################################################

inseq1 = <seq file 1>
inseq2 = <seq file 2>
outct = <output ct file for seq 1>
outct2 = <output ct file for seq 2>
aout = <output alignment file>

################################################################
# Options with default values if not explicitly specified
# (Default values are shown)
#################################################################

# fgap is the per nucleotide insert penalty for alignments:
fgap = .4

# maxtrace is the masximum number of predicted structures:
maxtrace = 750

# percent is the maximum % change in free energy from the lowest free energy structure:
percent = 20

# bpwin is the base pair window:
bpwin = 2

# awin is the alignment window:
awin = 1

# insert indicates whether single basepair inserts will be allowed:
insert = 1

# singlefold_subopt_percent is the maximum % difference in folding free energy change
# from single sequence folding for pairs that will be allowed in a subsequent Dynalign calculation.
# This is used to save calculation time by pre-screening allowed pairs. 
singlefold_subopt_percent = 30

# imaxseparation is the traditional M parameter:
# -99 indicates that the alignment constraint (preferred method is used)
imaxseparation = -99

# num_processor is required only for smp (parallel) calculations
num_processors = 1

# optimal only is optional, only the lowest free energy structure is calculated if optimal_only = 1
optimal_only = 0

# local folding is performed if local = 1, the default is 0 (global folding)
local = 0

# the following are needed for progressive calculations
# dsv_templated is set to 1 to read the template from previous calculation
dsv_templated = 0
dsvtemplatename = <template file name>

# The following are used to predict a structure for sequence 2, where the structure for sequence 1 is known.
# If ct_templated is set to 1, inseq1 must refer to a ct file, NOT a sequence file.
ct_templated = 0

# The following parameters are used when SHAPE data is utilized (see below).
# There is a set of parameters for each sequence.
shapeslope1 = 2.6
shapeintercept1 = -0.8
shapeslope2 = 2.6
shapeintercept2 = -0.8

################################################################
# Options that are not required and have no default values
################################################################

# Savefiles are optional and are needed for dot plots.
savefile = <save file name>

# Folding constraints can be input using constraint files:
constraint_1_file = <constraint file for seq 1>
constraint_2_file = <constraint file for seq 2>

# SHAPE data can be input using .shape files for either, neither, or both
# SHAPE is utilized using the pseudo free energy method of Deigan et al.
# PNAS 106:97
shape_1_file = <SHAPE file for seq 1>
shape_2_file = <SHAPE file for seq 2>

# Use constraint_align_file to enforce specific nucleotide alignments.
constraint_align_file = <alignment constraints file>

# Use maximumpairingdistance to limit the maximum distance between 
# paired nucleotides (where the final # indicates the sequence #).
# Note that this only works for sequence 1 if the calculation is not 
# cttemplated or dsvtemplated.
maximumpairingdistance1 = <value for seq 1>
maximumpairingdistance2 = <value for seq 2>
         

1. Reuter, J.S. and Mathews, D.H.
   "RNAstructure: software for RNA secondary structure prediction and analysis."
   BMC Bioinformatics, 11:129. (2010).
2. Harmanci, A.O., Sharma, G. and Mathews, D.H.
   "Efficient Pairwise RNA Structure Prediction Using Probabilistic Alignment Constraints in Dynalign."
   BMC Bioinformatics, 8:130. (2007)
3. Uzilov, A.V., Keegan, J.M. and Mathews, D.H.
   "Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change."
   BMC Bioinformatics, 7:173. (2006).
4. Mathews, D.H.
   In Baxevanis, A. D., Davison, D. B., Page, R. D. M., Petsko, G. A., Stein, L. D. and Stormo, G. D. (eds.).
   Current Protocols in Bioinformatics.
   John Wiley and Sons, Inc., New York, pp. 12.14.11-12.14.11. (2005).
5. Mathews, D.H.
   "Predicting a set of minimal free energy RNA secondary structures common to two sequences."
   Bioinformatics, 21:2246-2253. (2005).
6. Mathews, D.H. and Turner, D.H.
   "Dynalign: An algorithm for finding the secondary structure common to two RNA sequences."
   J. Mol. Biol., 317:191-203. (2002).