tatapov

Tatapov

Tatapov is a Python library making accessible and easy to explore the DNA overhang misannealing data from Potapov et al. (2018, ACS Synth. Biol. <https://pubs.acs.org/doi/10.1021/acssynbio.8b00333>) and Pryor et al. (2020, PLoS ONE <https://doi.org/10.1371/journal.pone.0238592>):

Comprehensive Profiling of Four Base Overhang Ligation Fidelity by T4 DNA Ligase and Application to DNA Assembly. 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. ACS Synth. Biol. (2018) 7, 11, 2665–2674.

Enabling 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.

The 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 example

Plotting

.. code:: python

import tatapov

Get a subset of the data at 25C (1h incubation)

data = tatapov.annealing_data["25C"]["01h"] # a pandas dataframe overhangs = ["ACGA", "AAAT", "AGAG"] subset = tatapov.data_subset(data, overhangs, add_reverse=True)

Plot the data subset

ax, _ = tatapov.plot_data(subset, figwidth=5, plot_color="Blues") ax.figure.tight_layout() ax.figure.savefig("example.png")

.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/tatapov/master/images/tatapov_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 the plot_color parameter.

The following datasets are available (see the publications for more details):

.. code:: python

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 overhangs

.. code:: python

import tatapov

annealing_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 = [
    overhang
    for overhang, self_annealing in relative_self_annealing.items()
    if self_annealing < 0.4
]

Identifying overhang pairs with significant cross-talking

.. code:: python

import tatapov

annealing_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_pair
    for overhang_pair, cross_annealing in cross_annealings.items()
    if cross_annealing > 0.08
]

Installation

You can install Tatapov through PIP:

.. code::

pip install tatapov

License = MIT

Tatapov is an open-source software originally written at the Edinburgh Genome Foundry by Zulko <https://github.com/Zulko>_ and released on Github <https://github.com/Edinburgh-Genome-Foundry/tatapov>_ under the MIT licence (Copyright 2018 Edinburgh Genome Foundry, University of Edinburgh).

More biology software

.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Edinburgh-Genome-Foundry.github.io/master/static/imgs/logos/egf-codon-horizontal.png :target: https://edinburgh-genome-foundry.github.io/

Tatapov is part of the EGF Codons <https://edinburgh-genome-foundry.github.io/>_ synthetic biology software suite for DNA design, manufacturing and validation.