MOTIVATION: Understanding gene regulation and expression is the key to the advancement of biology. EST sequence assembly and analysis provide unique benefits in this regard. We have developed a standalone application, dCAS (Desktop cDNA Annotation System), which performs automated EST cleaning, clustering, assembly and annotation on a desktop computer. Compared with other available tools, dCAS provides a more convenient and user-friendly solution to biologists for extracting biological meaning from sequence data. AVAILABILITY: The dCAS package is distributed freely. A cross-platform installer and associated sequence databases can be downloaded at: http://exon.niaid.nih.gov/applications.html.