seapovedac / cprisma

CPRISMA (version 1.0, 2021) is a bioinformatics program that gives color to multiple sequence alignment based on an input of numerical data.

CPRISMA is written by:

Sergio Alejandro Poveda Cuevas [email protected] Laboratory of Computational Biophysical Chemistry University of São Paulo, Ribeirão Preto - SP, Brazil

CPRISMA is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 3 (GPLv3).

CPRISMA (version 1.0, 2021) is a bioinformatics program that gives color to protein multiple sequence alignments based on an input of numerical data.

More details can be found in the user’s guide documentation found in the file "docs/CPRISMA user's guide - 2021.pdf".

Some similar examples of the possible outputs obtained with CPRISMA can be found on the next publications:

• Poveda-Cuevas, S.A.; Etchebest, C.; Barroso da Silva, F. L. Insights into the ZIKV NS1 Virology from Different Strains through a Fine Analysis of Physicochemical Properties. ACS Omega, 3(11), pp 16212–16229, 2018 (doi: https://doi.org/10.1021/acsomega.8b02081).

• Poveda-Cuevas, S.A.; Etchebest, C.; Barroso da Silva, F. L. Identification of Electrostatic Epitopes in Flavivirus by Computer Simulations: The PROCEEDpKa Method. ACS Journal of Chemical Information and Modeling, 60(2), pp 944–963, 2020 (doi: https://doi.org/10.1021/acs.jcim.9b00895).

• Poveda-Cuevas, S.A.; Barroso da Silva, F. L.; Etchebest, C. How the Strain Origin of ZIKV NS1 Protein Impacts its Dynamics and Implications to their Differential Virulence. ACS Journal of Chemical Information and Modeling, 61(3), pp 1516–1530, 2021, 2021 (doi: https://doi.org/10.1021/acs.jcim.0c01377).

• Poveda-Cuevas, S.A.; Etchebest, C.; Barroso da Silva, F. L. Self-association features of NS1 proteins from different flaviviruses. Virus Research, 318,198838, 2022 (doi: https://doi.org/10.1016/j.virusres.2022.198838).

Another sources:

*** If you use this program cite as: Poveda-Cuevas, S.A., 2021. CPRISMA (Coloring Proteins by Inputs and Sets of Multiple Alignments) software. https://github.com/seapovedac/cprisma. ***

Requirements

CPRISMA requires Python 3.7 or higher, Numpy, Pandas, and Argparse.

Installation

CPRISMA can be installed by downloading the source code or cloning the repository executing:

git clone https://github.com/seapovedac/cprisma.git

Then:

pip install .

Uninstallation

To uninstall CPRISMA you can invoke the next command:

pip uninstall cprisma

Getting started

CPRISMA can be executed invoking the command:

cprisma

or

python -m cprisma

A list of options can be visualized with the -h option:

cprisma -h

For the correct execution of the program, three different files should appear in the directory:

1) a python script called ‘array_get.py’,
2) the alignment to put the color called ‘alignment.dat’, and
3) a CSV file called ‘data_input.csv’.

The alignment data is based on outputs of the MUSCLE program in ClustalW format and the data of the CSV file can be any type of numerical information given in columns.

Examples

CPRISMA can be tested using the files in [examples/].

Some examples of images that can be generated by CPRISMA appear below.

a) Example 1: ∆pK_a for several NS1_ZIKV

b) Example 2: B-cell epitope predictions on NS1_{WNV(176−352)}

c) Example 3: Protein structural domains for two NS1_ZIKV and its biological interfaces

Additional documentation

Additional documentation can be found in the file "docs/CPRISMA user's guide - 2021.pdf".