Nikola Đorđević1,2, Ivan Skadrić3, Slaviša Stanković4, Zorica Knežević-Jugović2, Snežana Đorđević1
1 Agrounik ltd, Belgrade, Serbia
2 University of Belgrade – Faculty of Technology and Metallurgy
3 Klaren ltd, Belgrade, Serbia
4 University of Belgrade – Faculty of Biology
nikola.djordjevic [at] agrounik.rs
Abstract
To enhance modern laboratory workflow, we developed software with a graphical user interface (GUI) that automates BLAST analysis, creates, and displays phylogenetic trees for multiple sequences in FASTA format. This software features time-saving functionality that increases productivity in the identification of microorganisms based on both 16S and ITS analysis and matches them in reference databases on a local server.
Both the GUI and the software backend are written in Python and incorporate two key functions, perform_blast_analysis and create_phylogenetic_tree, which utilize methods from the BioPython library. The perform_blast_analysis function automates and optimizes BLAST analysis by utilizing methods from the Bio Blast subpackage to execute queries for multiple sequences and generate results in XML output format. Once generated, the results can be extracted from XML and saved as a CSV file, providing a detailed report containing information on the five best matching sequences, including query ID, sequence name, topic ID, bacterial type, identification percentage, alignment length, E-value, and score.
The create_phylogenetic_tree function automates phylogenetic analysis and visualization, starting with sequence alignment by the Muscle tool from the Bio Align subpackage. Genetic distance is estimated using methods from the Bio Phylo package with an ‘identity’ model, and the phylogenetic tree is constructed by the UPGMA algorithm. Visualization of the phylogenetic tree is performed using the matplotlib package, providing the user with a clear view of the genetic lineages. By integrating these steps, the application significantly speeds up screening analysis and automates the complex processes of microbial taxonomy determination and examination of evolutionary relationships based on DNA sequencing.
This application highlights the importance of intuitively developing a GUI with functions tailored for specific laboratory tasks, based on the integration of laboratory, bioinformatics, and software development experience. By implementing this software into laboratory workflows, a significant reduction in the time required to process FASTA files with multiple entries can be achieved.
Keywords: BLAST, Phylogenetic tree construction, Microbial identification