CT2DB
NAME
ct2db − manual page for ct2db 2.6.4
SYNOPSIS
ct2db [OPTIONS] [<input0.ct>] [<input1.ct>]...
DESCRIPTION
ct2db 2.6.4
Produce dot bracket notation of an RNA secondary structure from Zuker’s .ct file
This program
converts connectivity table (.ct) files into extended FASTA
format with dot−bracket string.
−h, −−help
Print help and exit
−V, −−version
Print version and exit
−p, −−no−pk
Remove pseudoknots from structure
(default=off)
−m, −−no−modified
Do not keep modified bases, i.e. replace all non−canonical nucleotides with N.
(default=off)
−v, −−verbose
Be verbose.
(default=off)
REFERENCES
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
REPORTING BUGS
If in doubt our program is right, nature is at fault. Comments should be sent to rna@tbi.univie.ac.at.