SeqDivA

Sequence Diversity Analysis

Authors

• Evys Ancede-Gallardo (eancedeg@gmail.com)
• Guillermin Agüero-Chapin (gaguero@gmail.com)

Sequence Diversity Analysis - SeqDivA version 1.0 is a python-based tool with a friendly GUI designed for Linux and Mac OS.

Utility: Run alignment algorithms (water, needle, and blast) to compare all-vs.-all protein, DNA, and RNA sequences. SeqDivA provides similarity, identity, and bit-score matrixes and dot plots to explore/illustrate the diversity (homology degree) of the sequences, enabling the delimitation of the twilight zone.

Installation Prerequisites:

•   matplotlib
  

•   numpy
  

•   pandas
  

•   pyqt
  

•   biopython
  

Installation:

•   Download SeqDivA at https://github.com/eancedeg/SeqDivA
  

•   decompress the “.zip or tar.gz” file
  

•   Load the graphical interface by executing python SeqDivA.py. Python 3.7 is recommended.
  

Authors:

•   Evys Ancede-Gallardo (eancedeg@gmail.com), Programa de Doctorado en Fisicoquímica Molecular, Facultad de Ciencias Exactas, Universidad Andrés Bello, Av. República 275, Santiago 8370146, Chile.
  

•   Guillermin Agüero-Chapin (gaguero@gmail.com), CIIMAR- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Portugal
  

Reference: Agüero-Chapin, G., Galpert, D., Molina-Ruiz, R., Ancede-Gallardo, E., Pérez-Machado, G., De la Riva, G. A., & Antunes, A. (2019). Graph Theory-Based Sequence Descriptors as Remote Homology Predictors. Biomolecules, 10(1), 26. https://doi.org/10.3390/biom10010026