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DynalignDotPlot is used to create a pairing energy dot plot for the structures of one of the two sequences folded by a Dynalign calculation.
USAGE: DynalignDotPlot <save file> <ps file> [options]
| <save file> |
The name of a binary Dynalign save file. These binary save files usually end in ".dsv", and contain probability data from a previous Dynalign calculation. |
| <output file> |
The name of a file to which output will be written.
Depending on the options selected, this may be one of the following file types.
1) A Postscript image file.
2) An SVG image file.
3) A plain text file.
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| -h, -H, --help |
Display the usage details message. |
| --s2, -S2, --sequence2 |
Use sequence 2, rather than the default of sequence 1. |
| --svg |
Specify that the output file should be an SVG image file, rather than a Postscript image file. |
| -t, -T, --text |
Write dot plot as a text file, rather than a Postscript image file. |
| -e, -E, --entries |
Specify the number of categories in the plot legend.
Default is 5 entries.
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| -max, -MAX, --maximum |
Specify the maximum value in the plot in kcal/mol.
Default is the largest valid value in the plot.
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| -min, -MIN, --minimum |
Specify the minimum value in the plot in kcal/mol.
Default is the smallest valid value in the plot.
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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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Mathews, D. H.
"Predicting a set of minimal free energy RNA secondary structures common to two sequences."
Bioinformatics, 21:2246-2253. (2005).
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