Block searches on VAX and Alpha computer systems

Abstract

A new program, BlockSearch, is described that allows biologists to search protein sequences against the BLOCKS database 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. Although written primarily for Digital's Alpha and VAX systems, the code is easily portable to other platforms.