BlockSearch allows biologists to search protein sequences against the BLOCKS databse of aligned protein blocks by converting these blocks to site-specific scoring matrices. It thus complements existing tools for standard similarity searches and pattern searches which aid in elucidating the function of newly determined protein-coding sequences. The speed of the program and the existence of a command-line interface render BlockSearch particularly interesting for the batch analysis of many new sequences, such as collections of expressed sequence tags. BlockSearch was written by Rainer Fuchs, EMBL. A paper describing BlockSearch has appeared in CABIOS 9 (1993), 587-591.