Novabrowse: A Tool for High-Resolution Synteny Analysis, Ortholog Detection, and Gene Signal Discovery

Abstract

Accurate genome annotation remains challenging as assembly quality often exceeds annotation reliability. Resolving ambiguities of gene presence, absence, and orthology typically requires integrating two complementary lines of evidence: sequence homology between species and the conservation of gene order (i.e., synteny). BLAST remains the standard for homology detection, yet its raw output can be difficult to interpret. Existing tools address this challenge but operate at opposing scales. Alignment viewers provide detailed pairwise statistics without genomic context, while synteny tools offer chromosome-scale perspectives without sequence-level resolution. To fill this intermediate gap, we developed Novabrowse, an interactive BLAST results interpretation framework featuring high-resolution multi-species synteny analysis, chromosomal re-arrangement investigation, ortholog detection, and gene signal discovery. Users define a genomic region of interest in a query species and/or use custom sequences, then select one or more subject species for comparison. The pipeline retrieves query gene sequences via NCBI API integration and performs BLAST searches against each subject transcriptome or genome. Results are presented via an interactive HTML file featuring alignment statistics, chromosomal maps, coverage visualizations, ribbon plots, and distance-based clustering of high-scoring segment pairs into putative gene units. We demonstrate these capabilities by investigating Foxp3, Aire, and Rbl1, three highly conserved vertebrate genes, in the recently assembled genome of the newt Pleurodeles waltl. Foxp3 and Aire have not been described in any salamander species to date, despite availability of multiple assemblies and extensive transcriptomic datasets. Using Novabrowse, we discovered conserved loci and gene signals for both genes in P. waltl, the presence of which was subsequently confirmed via Nanopore long-read RNA sequencing. In contrast, Rbl1 analysis uncovered a chromosomal rearrangement at its expected locus with no gene signal detected, indicating a gene loss specific to P. waltl despite the genes retention in the closely related axolotl (Ambystoma mexicanum). Our findings demonstrate Novabrowses capacity for evidence-based evaluation of annotation artifacts, an essential capability as high-quality assemblies become more available for phylogenetically diverse species. Novabrowse is open source (MIT license) and freely available at: https://github.com/RegenImm-Lab/Novabrowse.