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.

ct2db 2.6.4                                       January 2025                                          CT2DB(1)