REACTR: a Rapid Exploration And Characterization Tool for Research

Next-generation sequencing has produced an exponential increase in genomic data, yet functional characterization of newly discovered genes remains a significant bottleneck. Current approaches typically require manual integration of disparate web servers and standalone tools, a process that is time-consuming, difficult to reproduce, and prone to error. Here, we present reactr, an open-source, modularized, Snakemake workflow for automated, species-agnostic characterization of gene families from sequence to experimental design. Given a query protein sequence and NCBI taxonomy IDs (or RefSeq assembly accessions), reactr automatically retrieves reference genomes and executes comprehensive analysis across four main integrated tiers: (1) evolutionary analysis, including homolog detection, domain-based clustering, multiple sequence alignment, and phylogenetic inference; (2) synteny and selection analysis, detecting collinear blocks and calculating Ka/Ks ratios to assess evolutionary constraints; (3) structural and regulatory characterization, including motif discovery, chromosomal mapping, biochemical property prediction, subcellular localization prediction, and promoter analysis; and (4) experimental design tools, generating optimized PCR primers and scored CRISPR guide RNAs for laboratory validation. By seamlessly bridging computational prediction and experimental validation, reactr enables rapid transition from genomic discovery to functional studies.

Supported on MacOS and Linux. Example and validation outputs can be found here: https://dataverse.harvard.edu/dataverse/reactr