CT2DB

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 nucleotides 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 automaticall 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. (default=‘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.