PaGeSearch: A Tool for Identifying Genes within Pathways in Unannotated Genomes

Abstract

In biological research, the identification and comparison of genes within specific pathways across the genomes of various species are invaluable. However, annotating the entire genome is resource-intensive and sequence similarity searches often yield results that are not actually genes. To address these limitations, we introduce PaGeSearch (Pathway Gene Search), a tool designed to identify genes from predefined lists, especially those in specific pathways, within genomes. The tool employs an initial sequence similarity search to identify relevant genomic regions, followed by targeted gene prediction and neural network-based result filtering. PaGeSearch suggests the regions that are most likely the orthologs of the genes in the query and is designed to be applicable for species within five classes: mammals, fish, birds, eudicotyledons, and liliopsida. When compared with GeMoMa, PaGeSearch consistently outperformed in terms of sensitivity and positive predictive value. Although its performance showed increased variability when applied to actual biological pathways, it nonetheless maintained an acceptable level of accuracy.