Package: tatapov
TatapovTatapov is a Python library making accessible and easy to explore the DNA
overhang misannealing data from Potapov et al. (2018,bioRxiv) and Pryor et al. (2020,PLoS ONE):Optimization of Golden Gate assembly through application of ligation
sequence-dependent fidelity and bias profiling.Vladimir Potapov,
Jennifer L. Ong, Rebecca B. Kucera, Bradley W. Langhorst,
Katharina Bilotti, John M. Pryor, Eric J. Cantor, Barry Canton,
Thomas F. Knight, Thomas C. Evans Jr., Gregory Lohman. bioRxiv (2018)https://doi.org/10.1101/322297Enabling one-pot Golden Gate assemblies of unprecedented complexity using
data-optimized assembly design.John M. Pryor, Vladimir Potapov,
Rebecca B. Kucera, Katharina Bilotti, Eric J. Cantor, Gregory J. S. Lohman.
PLoS ONE (2020) 15(9): e0238592.https://doi.org/10.1371/journal.pone.0238592The Supplementary Material of these papers provide tables of inter-overhang
annealing data in various conditions (01h or 18h incubations at 25C or 37C).
Tatapov provides these tables (it will download them automatically
upon first use) as pandas dataframes, so that they are easy to manipulate.It also provides simple methods to build and plot subsets of the data (plotting
requires Matplotlib installed).Usage examplePlottingimporttatapov# Get a subset of the data at 25C (1h incubation)data=tatapov.annealing_data["25C"]["01h"]# a pandas dataframeoverhangs=["ACGA","AAAT","AGAG"]subset=tatapov.data_subset(data,overhangs,add_reverse=True)# Plot the data subsetax,_=tatapov.plot_data(subset,figwidth=5,plot_color="Blues")ax.figure.tight_layout()ax.figure.savefig("example.png")In the plot above, if you see anything else than the square pairs around the
diagonal, it means there is cross-talking between your overhangs (so risk of misannealing).
If one of these diagonal square pairs appears lighter than the others, it means that
the corresponding overhang has weak self-annealing (risk of having no assembly).
A color square in the diagonal means that the overhang can anneal with itself (palindromic).
The Matplotlib colormap is specified with theplot_colorparameter.The following datasets are available (see the publications for more details):# Potapov 2018:tatapov.annealing_data[temperature][time]# where temperature is '25C' or '37C', and time is '01h' or '18h'# Pryor 2020 (all 01h):tatapov.annealing_data['37C'][enzyme]# where enzyme is one of:# '2020_01h_BsaI', '2020_01h_BsmBI', '2020_01h_Esp3I' or '2020_01h_BbsI'Identifying weak self-annealing overhangsimporttatapovannealing_data=tatapov.annealing_data['37C']['01h']# Compute a dictionary {overhang: self-annealing score in 0-1}relative_self_annealing=tatapov.relative_self_annealings(annealing_data)weak_self_annealing_overhangs=[overhangforoverhang,self_annealinginrelative_self_annealing.items()ifself_annealing<0.4]Identifying overhang pairs with significant cross-talkingimporttatapovannealing_data=tatapov.annealing_data['37C']['01h']# Compute a dictionary {overhang_pair: cross-talking score in 0-1}cross_annealings=tatapov.cross_annealings(annealing_data)high_cross_annealing_pairs=[overhang_pairforoverhang_pair,cross_annealingincross_annealings.items()ifcross_annealing>0.08]InstallationYou can install Tatapov through PIP:pip install tatapovAlternatively, you can unzip the sources in a folder and typepython setup.py installLicense = MITTatapov is an open-source software originally written at the Edinburgh Genome
Foundry byZulkoandreleased on Githubunder the MIT licence (Copyright 2018 Edinburgh Genome Foundry). Everyone is welcome
to contribute !Please contact us if there is any issue regarding copyright (there shouldn’t be
as the repository does not contain any data, and the paper data is free to
download).More biology softwareTatapov is part of theEGF Codonssynthetic biology software suite for DNA design, manufacturing and validation.