drawtetrado 1.1

Draw simplified, layer diagrams of quadruplexes.

Project description

DrawTetrado is a Python application to visualize quadruplexes and G4-helices in DNA and RNA structures. It generates publication-quality SVG files containing layer diagrams. They show the tetrads as a stack, with each position having four nucleobases colored according to anti or syn conformation. In addition, DrawTetrado visualizes the strands with arrows for an accessible overview of their directionality and visual determination of loop types.

DrawTetrado automatically optimizes the layout. The result is a visually pleasing and readable image, even for the most complex cases like V-loops and G4-helices (dimers).

Installation

pip install drawtetrado

Dependencies

The project is written in Python 3.6+ and requires pycairo and svgwrite. The internal optimization routine is written in C++ and requires Cython and a C++20-compliant compiler (e.g. GCC 8+).

DrawTetrado parses the output of ElTetrado (Zok et al., 2022; Popenda et al., 2020; Zok et al., 2020). If you do not have that installed, please install DSSR (Lu et al., 2015) and run:

pip install eltetrado

Usage

usage: drawtetrado [-h] input output

positional arguments:
  input       path to input JSON generated by ElTetrado
  output      path to output SVG file template

options:
  -h, --help  show this help message and exit

The output path is a template. For example, if output=/tmp/out.svg, the
resulting files will be /tmp/out_0.svg, /tmp/out_1.svg and so on (for as many
distinct quadruplexes as there are in the input file)

Examples

Human telomere DNA quadruplex

V-loop

G4-helix (dimer)

Bibliography

1. ONQUADRO: a database of experimentally determined quadruplex structures. T. Zok, N. Kraszewska, J. Miskiewicz, P. Pielacinska, M. Zurkowski, M. Szachniuk. Nucleic Acids Research. 2022. 50(D1):D253–D258. doi:10.1093/nar/gkab1118

2. Topology-based classification of tetrads and quadruplex structures. M. Popenda, J. Miskiewicz, J. Sarzynska, T. Zok, M. Szachniuk. Bioinformatics. 2020. 36(4):1129–1134. doi:10.1093/bioinformatics/btz738

3. ElTetrado: a tool for identification and classification of tetrads and quadruplexes. T. Zok, M. Popenda, M. Szachniuk. BMC Bioinformatics. 2020. 21(1):40. doi:10.1186/s12859-020-3385-1

4. DSSR: an integrated software tool for dissecting the spatial structure of RNA. X.-J. Lu, H.J. Bussemaker, W.K. Olson. Nucleic Acids Research. 2015. 43(21):e142. doi:f73r8c