Connectivity Table (CT): RNA secondary structures

CT file: Content format

In a CT file, each RNA structure record comprises two parts:

  • A header that contains the name and length of the structure.

  • A body that contains the structure.

See CT format for more information.

CT header line

Every header line must start with the length of the structure, delimited by whitespace. Thereafter, from the first non-whitespace character to the end of the line is the title of the structure.

CT body lines

The remaining lines in each record encode the structure. SEISMIC-RNA can parse sequences that obey the following rules:

  • Every body line comprises six whitespace-delimited fields:

    1. Index in the region

    2. Base

    3. Previous (index minus 1), or 0 if the first index

    4. Next (index plus 1), or 0 if the last index

    5. Index of the pairing partner, or 0 if unpaired

    6. Position in the reference sequence

  • The indexes must be contiguous positive integers beginning at 1.

  • The base must be A, C, G, U, or N.

  • The positions must be contiguous positive integers.

CT file: Path format

CT file extensions

SEISMIC-RNA accepts the following extensions for CT files:

  • .ct

CT path parsing

Every output CT file is named after its mutational profile, but names of input CT files are not used for any purpose.

CT file: Uses

CT as input file

Structures for these commands must be input as CT files:

  • seismic graph roc

  • seismic renumct

CT as output file

  • The fold command outputs a CT file for each predicted structure.

  • The renumct command outputs a renumbered CT file for each input CT file.

CT as temporary file

  • The fold command writes a temporary CT file from Fold, which it then renumbers.