This tool is designed to quickly match large sets of patterns against biosequence databases and is optimized for multi-processor computers. Biogrep uses standard POSIX extended regular expressions and can divide the pattern-matching task between a user-specified number of processors.
Biogrep is written in the C programming language using the GNU regular expression (Hargreaves & Berry, 1992) and POSIX threads (pthreads) (Mueller, 1993) libraries. The program reads query patterns from either a plain text file, one-per-line, or from a Teiresias-formated pattern file (Rigoutsos & Floratos, 1998). These patterns are treated as POSIX extended regular expressions and are searched against a user supplied file, which can be either a FastA (Pearson & Lipman, 1988) formatted biosequence database or any text file.
For more info, read this Biogrep documentation.
Kyle
kljensen@gmail.com