Dot-bracket (DB): RNA secondary structures
DB file: Content format
In a DB file, each RNA structure record comprises two parts:
A header that contains the name of the structure.
A body that contains the structure on one line (and for only the first structure, the RNA sequence on the line before).
See DB format for more information.
DB header line
The first line of each structure record is the name of the structure.
DB body lines
For the first structure, the line after the header is the RNA sequence, which can contain A, C, G, U, and N.
The structure is encoded on one line as a series of dots (.) and
brackets ((/), [/], {/}, </>).
A dot indicates that the base does not pair with another base.
A bracket indicates that the base pairs with the matching bracket.
DB file: Path format
DB file extensions
SEISMIC-RNA accepts the following extensions for dot-bracket files:
.db(default).dbn.dot
DB path parsing
Every output DB file is named after its mutational profile.
DB file: Uses
DB as output file
The
foldcommand outputs a DB file for each predicted structure.