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ct2db − manual page for ct2db 2.4.16


ct2db [OPTION]... [FILE]...


ct2db 2.4.16

Produce dot bracket notation of an RNA secondary structure from Zuker’s .ct file

Convert Zuker’s .ct files to dot−bracket string
, −−help

Print help and exit

−V, −−version

Print version and exit

−p, −−removePK

Remove pseudoknots from structure (default=off)

−c, −−convertToRNA

Substitute all nucleotides with their RNA alphabet counter parts, i.e. convert to characters A, C, G, U or N for unknown bases.


−v, −−verbose

Be verbose (default=off)


If you use this program in your work you might want to cite:

R. Lorenz, S.H. Bernhart, C. Hoener zu Siederdissen, H. Tafer, C. Flamm, P.F. Stadler and I.L. Hofacker (2011), "ViennaRNA Package 2.0", Algorithms for Molecular Biology: 6:26

I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994), "Fast Folding and Comparison of RNA Secondary Structures", Monatshefte f. Chemie: 125, pp 167-188

R. Lorenz, I.L. Hofacker, P.F. Stadler (2016), "RNA folding with hard and soft constraints", Algorithms for Molecular Biology 11:1 pp 1-13


If in doubt our program is right, nature is at fault. Comments should be sent to