Evolutionary analysis of gene networks with Orthoweb software
2022
Motivation and Aim: Phylostratigraphic analysis is a new trend in evolutionary analysis, aimed to determine the time of gene origin The method based on analysis of taxonomic classification of genes and their orthologs and finding the common taxon. With such method of sequences analysis, as dN/dS ratio The methods of such analysis, implemented in different software packages (myTAI [3], phylostratr [4], Orthoscape [5], etc.), require the user to know the programming languages (mostly R) or how to use another software, like Cytoscape Most methods also aimed to analyze the gene lists, but it is interesting to look not only to genes, but also to their interactions and possible clusters in gene networks. Methods and Algorithms: Orthoweb software has been developed in the Java programming language. To develop the server part, we used the Spring framework; VueJS and Webix frameworks have been used for the client part. Networks visualizing is implemented with cytoscape.min.js library. The document-oriented database MongoDB is used to store the data from KEGG database (taxa, list of orthologous, coding sequences, etc.) and intermediate analysis results. It is significally increases the speed of future work with the same data. To store the result of analysis, we have developed the PostgreSQL database. Using REST API, the user can retrieve the data from previous analysis of gene with exactly same parameters.