ability to add pseudouridine and methylated positions

[Andrew Uzilov]

Many RNAs like tRNA, snRNA U1, etc. have modified nucleotides like
pseudouridine (denoted with Greek letter "psi") and 2'-O-methylated
bases (denoted with something like Cm). It would be good to have an
ability to specify these special characters from the applet. For
example, maybe I could write:

<param name='sequenceDBN' value='AA{Gm}AC{psi}AUA'>

and VARNA could draw base G3 by squeezing "Gm" and base U6 with a Psi
symbol. Here is an example figure showing many more diverse chemical
modifications:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2584109/figure/F1/

The whole set of those is overkill, but at the very least specifying a
pseudo-U and a 2'-O-me would be really useful.

[Yann Ponty]

At the risk of repeating myself, this is again an excellent idea.
However, this is also really tricky...

Indeed, printing out "Psi" as a greek letter will be fine within Java
and SVG using UTF-8 character encoding, but will not be as easily
treated within an EPS export. For the sub/super-scripts, UNICODE
chars are available only for certain characters (but it should be ok
for most purpose):
http://en.wikipedia.org/wiki/Unicode_subscripts_and_superscripts
I'm almost finished implementing an extended syntax (directly
inspired
by your example, and borrowing a bit to Latex), where you could write
such
stuffs as:
ACG{G_m}UUU{\psi}AA{m^1I}...
where anything between brackets will be assigned to a single base, '_'
puts
what follows in subscript, '^' in superscript and a bunch of "\cmd"
macros
will be available for special characters. Certain chars might be
unavailable
though...

Best and thanks for the suggestion,

Yann