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CT2DB(1)			  User Commands 			CT2DB(1)

NAME
     ct2db - manual page for ct2db 2.7.2

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

DESCRIPTION
     ct2db 2.7.2

     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)

     --fasta-header=STRING
	    Overwrite FASTA header with user-provided string.

	    The  name of the sequence (+structure pair) is usually extracted au-
	    tomaticall from the connectivity table header. Whenever such name is
	    not present or the user wants to replace  the  sequence  identifier,
	    this parameter option can be used to do exactly that. Note, however,
	    that for multiple structures in the input the same FASTA header will
	    appear for all of the FASTA output lines.

     --fh-from-filename[=replace|prepend|append]
	    Use input file name as output FASTA header.

	    (default=`replace')

	    This  only	works when the input is not stdin but actual file names.
	    By default, any (default) FASTA  header  will  be  replaced  by  the
	    (truncated)  input	file  name. Use the optional arguments "prepend"
	    and "append" if you want the existing FASTA header to  be  prepended
	    or appended by the input file name instead.

     --filename-suffix=STRING
	    The filename suffix to remove when turning the filename into a FASTA
	    header.

	    (default=`.ct')

	    Provide an empty string to not truncate the filename at all.

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

	    By	default,  any  log messages are filtered such that only warnings
	    (level 2) or errors (level 3) are printed. This setting  allows  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 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 2.7.2			  December 2025 			CT2DB(1)

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