ebFRET trace files

ebFRET trace files are ASCII files with the extension .dat. They are usually found in the main/video_processing/intensities/traces_ebFRET or main/traces_processing/traces_ebFRET analysis folder.

Table of contents

  1. Description
  2. File name
  3. Structure
  4. Compatibility
  5. References

Description

These trace files are written in an ASCII format importable in the software ebFRET [1]. Each file contains intensity-time traces of a specific FRET pair, integrated from a single molecule video (SMV) or exported after trace processing.

They are created in the /video_processing/intensities/traces_ebFRET analysis sub-folder after creating and exporting ebFRET traces in panel Intensity integration of module Video processing, or in or /traces_processing/traces_ebFRET if exported from panel Sample managementof module Trace processing.

File name

The file is named by the user during the export process.

By default, the file is named after the video file loaded in Video processing or the project file in Trace processing from which data are exported, and is appended with an extension _all[N]FRET[D]to[A]_ebFRET where [N] is the number of single molecules, and where [D] and [A] the channel indexes where donor and acceptor fluorescence are specifically detected.

Structure

FRET pair-specific intensity-time traces are organized row-wise by appending the same columns for each molecule, and column-wise with molecule indexes written in column 1, donor intensities in column 2 and acceptor intensities in column 3.

1	1.076712e+04	2.959472e+03
1	6.776125e+03	1.706861e+03
1	9.744125e+03	1.914148e+03
1	6.183125e+03	1.632889e+03

For consistency, intensity-time traces exported from module Video processing or Trace processing are always given as the sum of the brightest pixel intensities per video frame, regardless the units defined in Pixel intensity units or Intensity units respectively.

Compatibility

ebFRET trace files can be imported in external software ebFRET [1] and in MASH’s module Trace processing by adjusting the Import options to the actual file structure.

References

  1. J.W. van de Meent, J.E. Bronson, C.H. Wiggins, R.L. Gonzalez Jr, Empirical Bayes methods enable advanced population-level analyses of single-molecule FRET experiments, Biophys. J. 2013, DOI: 10.1016/j.bpj.2013.12.055