RT Journal Article
SR Electronic
T1 FRETBursts: Open Source Burst Analysis Toolkit for Confocal Single-Molecule FRET
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 039198
DO 10.1101/039198
A1 Antonino Ingargiola
A1 Eitan Lerner
A1 SangYoon Chung
A1 Shimon Weiss
A1 Xavier Michalet
YR 2016
UL http://biorxiv.org/content/early/2016/03/11/039198.abstract
AB Single-molecule Förster Resonance Energy Transfer (smFRET) allows probing intermolecular interactions and conformational changes in biomacromolecules, and represents an invaluable tool in studying cellular processes at the molecular scale [21]. smFRET experiments can detect the distance between two fluorescent labels (donor and acceptor) in the 3-10 nm range. In the commonly employed confocal geometry, molecules are free to diffuse in solution. When a molecule traverses the excitation volume it emits a burst of photons that can be detected by single-photon avalanche detectors (SPADs). The intensities of donor and acceptor fluorescence can then be related to the distance between the two dyes.The analysis of smFRET experiments involves identifying photon bursts from single-molecules in a continuous stream of photon, estimating the background and other correction factors, filtering and finally extracting the corrected FRET efficiencies for each sub-population in the sample. In this paper we introduce FRETBursts, a software for confocal smFRET data analysis which allows executing a complete burst analysis pipeline by using state-of-the-art algorithms. FRETBursts is an open source python package that we envision both as toolkit for research and new developments in burst analysis and as reference implementation of commonly employed algorithms. We follow the highest standard in software development to ensure that the source is easy to read, well documented and thoroughly tested. Moreover, in an effort to lower the barriers to computational reproducibility, we embrace a modern workflow based on Jupyter notebooks that allows to capture of the whole process from raw data to figures within a single document.