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]
||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.
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.
|-h, -H, --help
||Display the usage details message.
|--s2, -S2, --sequence2
||Use sequence 2, rather than the default of sequence 1.
||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.
|-max, -MAX, --maximum
Specify the maximum value in the plot in kcal/mol.
Default is the largest valid value in the plot.
|-min, -MIN, --minimum
Specify the minimum value in the plot in kcal/mol.
Default is the smallest valid value in the plot.
Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction and analysis."
BMC Bioinformatics, 11:129. (2010).
Mathews, D. H.
"Predicting a set of minimal free energy RNA secondary structures common to two sequences."
Bioinformatics, 21:2246-2253. (2005).