VARNA Color: Color codes for VARNA

If you draw RNA structures using the software VARNA, then you can use VARNA color files to color the bases by their mutation rates.

VARNA color file: Content format

Each line of a VARNA color file corresponds to one position in the RNA sequence you folded. For each position that has data (i.e. is within the region from which the data came and was not masked), the line has the normalized mutation rate, which is a decimal number between 0 and 1 (inclusive). For every position without data, the line just has the value -1.

VARNA color file: Path format

VARNA color file extensions

SEISMIC-RNA accepts the following extensions for VARNA color files:

• .txt

VARNA color path parsing

Every output VARNA color file is named after its mutational profile, plus __varna-color.txt at the end.

VARNA color file: Uses

VARNA color as output file

• The Fold step outputs a VARNA color file for each predicted structure.