SequenceServer is a Ruby/Sinatra web application that provides a graphical interface for running NCBI BLAST+ and DIAMOND sequence similarity searches against custom databases. It manages BLAST database formatting, job submission with background execution, result parsing, and interactive visualization of alignments using D3.js and Circos-style plots. The backend uses a thread pool for concurrent job processing, YAML-based job persistence, and a plugin system for extensibility. The frontend is built with React and includes components for database selection, query input, and result exploration with export to SVG/PNG. The application is designed for bioinformatics researchers who need a self-hosted BLAST server with a modern web UI, supporting multiple BLAST programs (blastn, blastp, blastx, tblastn, tblastx) and DIAMOND. It includes comprehensive test suites for multiple BLAST versions and CI/CD pipelines for Docker and AppImage deployment.