question on base pair style

[jiashiun]

Hi!

I'm a graduate student from Universiti Kebangsaan Malaysia.

I don't quite understand the Leontis/Westhof base pair style used in
the program. It uses the symbols "=” for GC pairs, "-" for GU pairs
and single line with a dot for BOTH AU pairs and non-canonical base
pairs. The symbols are different from what have been described in
Leontis & Westhof paper. Shouldn't it be "=" for GC pairs, "-" for AU
pairs, single circle for wobble GU pairs, and other symbols for non-
canonical base pairs?

Regards,
jiashiun

[Yann Ponty]

Dear Jiashiun,

Thanks for reporting this.
Actually, there is a bit of slack in the Leontis/Westhof
recommendation
(http://rnajournal.cshlp.org/content/7/4/499.long)
with two alternative ways to represent to represent canonical WC/WC.

VARNA's implementation borrows to both of them which, I guess, is not
really satisfactory :(

I just implemented your suggestion, and the fix will be available in
the upcoming version.
I guess send you a development snapshot it that can make your life
easier.

Best,

Yann