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CT2DB(1)			 User Commands			      CT2DB(1)

NAME
       ct2db - manual page for ct2db 2.7.0

SYNOPSIS
       ct2db [OPTIONS] [<input0.ct>] [<input1.ct>]...

DESCRIPTION
       ct2db 2.7.0

       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

       --detailed-help
	      Print help, including all	details	and hidden options, and	exit

       --full-help
	      Print help, including hidden options, 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  nu-
	      cleotides	with N.

	      (default=off)

       -v, --verbose
	      Be verbose.

	      (default=off)

       --log-level=level
	      Set log level threshold.	(default=`2')

	      By  default,  any	log messages are filtered such that only warn-
	      ings (level 2) or	errors (level 3) are printed. This setting al-
	      lows for specifying the log level	threshold, where higher	values
	      result in	fewer information. Log-level 5 turns off all messages,
	      even errors and other critical information.

       --log-file[=filename]
	      Print  log  messages  to	a  file	 instead  of   stderr.	  (de-
	      fault=`ct2db.log')

       --log-time
	      Include time stamp in log	messages.

	      (default=off)

       --log-call
	      Include file and line of log calling function.

	      (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	Struc-
       tures", 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 2.7.0			 October 2024			      CT2DB(1)

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