Software
smFRET Package
This package is associated with Roy et al, Nature Methods (2008).
Our software package for smFRET and example smFRET data are available for download on Lab GitHub.
HaMMy (Sean McKinney)
This package is associated with McKinney et al, Biophysical Journal (2006).
Our code treats single-molecule time-binned FRET trajectories as hidden Markov processes, allowing one to determine the most likely FRET-value distributions of states and their interconversion rates based on probability alone. Source code available upon request.
HaMMy (and TDP (transition density plot) generator) is available for download on Lab GitHub.
smCamera2 Package (Kyung Suk Lee/Taekjip Ha)
This is a Windows distribution that combines data acquisition and analysis into one program. Available on GitHub.
Lab GitHub
https://github.com/Ha-SingleMoleculeLab/
DNA cyclizability prediction (Jonghan Park & Sophia Yan)
https://cyclizability-prediction-website-5vbkhabttypl6n29hkxc8q.streamlit.app/
This builds on our previous work on measuring DNA mechanics on the genome scale and deciphering the mechanical code. You can either enter your sequence or a pdb of a DNA protein complex. For the latter, you will see the structure overlaid with the preferred direction of DNA bending, deduced from the DNA sequence alone. Documentation can be found below.
GitHub - codergirl1106/Cyclizability-Prediction-Website
Three-color smFRET analysis (Ashlee Feng)
This package was associated with Poyton, Feng et al, Science Advances (2022)
https://github.com/ashleefeng/singlemolecules/tree/master/smfret3color
https://zenodo.org/records/5804752
GOLD FISH (Yanbo Wang & Ashlee Feng)
These scripts are associated with Wang et al, Molecular Cell (2021) & Wang, Cottle et al, Nature Communications (2022).
https://github.com/ashleefeng/cas9
https://github.com/ywang285/NuclearEdge
PEG slide guide
PEG Protocol and Movie
PEG protocol as of September 2005
From Supplementary Information found in Rahul Roy, Sungchul Hohng, Taekjip Ha. “A practical guide to single-molecule FRET” Nature Methods (2008)
Intranet
You need Boston Children Hospital Google account (firstname.lastname@enders.tch.harvard.edu) to access the internal website and lab Google drive resources for the Ha-Myong laboratory.
https://sites.google.com/enders.tch.harvard.edu/hamyonglab/home
https://drive.bchresearch.org/
For lab members who need to create BCH Google account, use this link when you are on BCH network.