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AlignmentFold is used to predict the lowest free energy structure and a
set of suboptimal structures, i.e. low free energy structures,
for a structure conserved in a set of aligned homologs.
AlignmentFold-smp is the parallel version for use on multi-core computers.
USAGE: AlignmentFold <alignment file> <CT file> [options]
OR: AlignmentFold-smp <seq file> <ct file> [options]
| <alignment file> |
The name of an inputfile containing multiple sequence alignment of homologous RNA sequences in FASTA format. |
| <ct file> |
The name of a CT file to which output will be written. The CT file will show the first sequence of the input alignment.
If the --bracket flag is present, output will be written as a dot-bracket file.
If the file name is a hyphen (-), the structure will be written to standard
output (STDOUT) instead of a file. |
| --disablecoax |
Specify that coaxial stacking recusions should not be used. This option uses a less realistic energy function in exchange for a faster calculation. |
| -h, --help |
Display the usage details message. |
| -k, --bracket |
Write the predicted structure in dot-bracket notation (DBN) instead of CT format. |
| -mfe, -MFE, --MFE |
Specify that only the minimum free energy structure is needed.
No savefiles can be generated.
This saves nearly half the calculation time, but provides less information. |
| -q, --quiet |
Suppress unnecessary output. This option is implied when the output file is '-' (STDOUT). |
| -v, --version |
Display version and copyright information for this interface. |
| -b, -B, --bpcutoff |
Specify the base pairing cutoff.
Default is 0.3 |
| -l, -L, --loop |
Specify a maximum internal/bulge loop size.
Default is 40 unpaired nucleotides. |
AlignmentFold-smp, by default, will use all available compute cores for
processing. The number of cores used can be controlled by
setting the OMP_NUM_THREADS environment variable.
- Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction
and analysis."
BMC Bioinformatics, 11:129. (2010).
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