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RNAstructure Command Line Help |
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dynalign is used to find the lowest free energy common secondary structures for two homologous sequences. It has two distinct executables, a serial program called dynalign and a parallelized program called dynalign-smp for use in shared memory environments. dynalign_ii supercedes dynalign and should be used fo rmost applications. dynalign_ii allows inserts of structural domains that appear in only one of the two homologs. dynalign_ii also allows unpaired nucleotides to align to paired nucleotides. dynalign_ii-smp is a parallelized version for shared memory environments.
Note that on Macintosh OS X, and some versions of Linux, there is a small default stack limit. To run Dynalign/Dynalign II, the stack limit needs to be increased. USAGE 1: dynalign_ii <configuration file>USAGE 2: dynalign_ii-smp <configuration file>
USAGE 1: dynalign <configuration file>USAGE 2: dynalign-smp <configuration file>Required parameters:
Options which do not require added values:NONEOptions that require added values:NONEdynalign_ii configuration file format:
The following is a description of valid options allowed in the configuration file.
################################################################ # IMPORTANT CONFIG FILE FORMAT NOTES: # # Config file options described below are not case sensitive. # # Option lines may be specified by the option name followed by an equals sign and the option's desired value. # When specifying an option, there may be nothing else on the line. # If an option is specified more than once, the last specification is used. # <option> = <value> # # Specifying comment lines: # Comment lines must begin with "#" followed by a space. # There may not be more than one "#" in a comment line. # However, a comment line may be an unbroken string of "#", as in a divider between sets of options. # # Blank lines are skipped. # Any leading or trailing whitespace is ignored. # Variables may not contain internal whitespace. # # Syntax errors produce a warning to standard output and are then ignored. ################################################################ ################################################################ # Required input # If one of these values is not defined, the program will exit. ################################################################ #These are required input: inseq1 = RD0260.seq inseq2 = RD0500.seq outct = 1.ct outct2 = 2.ct aout = ali.ali ################################################################ # Options with default values if not explicitly specified # (Default values are shown) ################################################################# #fgap is the per nucleotide insert penalty for alignments: fgap = .4 #slope is the per nucleotide free energy penalty for inserted domains slope = 0.1 #intercept is the initiation free energy penalty for inserted domains intercept = 0.5 #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 #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 #max_elongation is the maximum length of a consecutive set of base pairs aligned with an internal loop with the same length max_elongation = 5 #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 alignment is performed if local = 1, the default is 0 (global alignment) 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 = RD0260.RD0500.dsv #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 = 1.8 #shapeintercept1 = -0.6 #shapeslope2 = 1.8 #shapeintercept2 = -0.6 #The following can be used to run Dynalign using DNA thermodynamics instead of RNA. #Use DNA = 1 to do DNA structure prediction. DNA = 0 #The following is used to change the temperature from the default of 310.15 K (37 degrees C). temperature = 310.15 ################################################################ # Options that are not required and have no default values ################################################################ #savefiles are optional and are needed for dot plots # savefile = RD0260.RD0500.dsv #Folding constraints can be input using constraint files: #constraint_1_file = constraints_for_sequence1 #constraint_2_file = constraints_for_sequence2 #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_for_sequence1 #shape_2_file = shape_for_sequence2 #Use constraint_align_file to enforce specific nucleotide alignments #constraint_align_file = aln.txt #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 = 600 #maximumpairingdistance2 = 600 dynalign configuration file format:The following is a description of valid options allowed in the configuration file. The example is based on dynalign_sample.conf, a standard example found in the examples directory of the RNAstructure repository. ################################################################ # IMPORTANT CONFIG FILE FORMAT NOTES: # # Config file options described below are not case sensitive. # # Option lines may be specified by the option name followed by an equals sign and the option's desired value. # When specifying an option, there may be nothing else on the line. # If an option is specified more than once, the last specification is used. # <option> = <value> # # Specifying comment lines: # Comment lines must begin with "#" followed by a space. # There may not be more than one "#" in a comment line. # However, a comment line may be an unbroken string of "#", as in a divider between sets of options. # # Blank lines are skipped. # Any leading or trailing whitespace is ignored. # Variables may not contain internal whitespace. # # Syntax errors produce a warning to standard output and are then ignored. ################################################################ ################################################################ # Required input # If one of these values is not defined, the program will exit. ################################################################ 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 alignment is performed if local = 1, the default is 0 (global alignment) 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 = 1.8 shapeintercept1 = -0.6 shapeslope2 = 1.8 shapeintercept2 = -0.6 # The following can be used to run Dynalign using DNA thermodynamics instead of RNA. # Use DNA = 1 to do DNA structure prediction. DNA = 0 # The following is used to change the temperature from the default of 310.15 K (37 degrees C). temperature = 310.15 ################################################################ # 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> Comparison of configuration file format:dynalign_ii added parameters slope, intercept, and max_elongation, which apply only to dynalign_ii calculations. dynalign has a parameter, insert, which no longer applies to dynalign_ii. References:
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