The Program RNAplot


You can manually add additional annotation to structure drawings using the RNAplot program (for information see its man page). Here’s a somewhat complicated example:

$ RNAfold 5S.seq > 5S.fold
$ RNAplot --pre "76 107 82 102 GREEN BFmark 44 49 0.8 0.8 0.8 Fomark \
  1 15 8 RED omark 80 cmark 80 -0.23 -1.2 (pos80) Label 90 95 BLUE Fomark" < 5S.fold
$ gv

PostScript macros

RNAplot is a very useful tool to color structure layout plots. The --pre tag adds PostScript code required to color distinct regions of your molecule. There are some predefined statements with different options for annotations listed below:



i cmark

draws circle around base i

i j c gmark

draw basepair i,j with c counter examples in grey

i j lw rgb omark

stroke segment i…j with linewidth lw and color (rgb)

i j rgb Fomark

fill segment i…j with color (rgb)

i j k l rgb BFmark

fill block between pairs i,j and k,l with color (rgb)

i dx dy (text) Label

adds a textlabel with an offset dx and dy relative to base i

Predefined color options are BLACK, RED, GREEN, BLUE, WHITE but you can also replace the value to some standard RGB code (e.g. 0 5 8 for lightblue).

To simply add the annotation macros to the PostScript file without any actual annotation you can use the following program call

$ RNAplot --pre "" < 5S.fold

If you now open the structure layout file with a text editor you’ll see the additional macros for cmark, omark, etc. along with some show synopsis on how to use them. Actual annotations can then be added between the lines:

% Start Annotations


% End Annotations

Here, you simply need to add the same string of commands you would provide through the --pre option of RNAplot.