Using the Job Dispatcher Web Interfaces for Sequence Analysis

The rapid growth of biological sequence data has increased the need for easy, accessible, and scalable tools for sequence comparison and analysis. The EMBL-EBI Job Dispatcher framework helps meet this need by providing a single web-based platform that offers many commonly used tools, including the BLAST, Clustal Omega, and EMBOSS programs. In this article, we provide a practical, easy-to-follow guide to the main tool categories available in Job Dispatcher, focusing on multiple sequence alignment and sequence similarity search. We present step-by-step workflows that demonstrate how to run these analyses directly on the web without installing any bioinformatics software. Our goal is to provide a simple, practical reference for researchers and students new to bioinformatics, helping them choose the right tools and use web-based analysis effectively. © 2026 EMBL-EBI. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Sequence similarity search using FASTA Basic Protocol 2: Sequence similarity search using NCBI BLAST+ Basic Protocol 3: Sequence similarity search using PSI-BLAST Basic Protocol 4: Multiple sequence alignment using Clustal Omega Basic Protocol 5: Visualizing multiple sequence alignments using MView Basic Protocol 6: Workflow from BLAST results to Clustal Omega to MView.