Creating protein sequence patterns using efficient regular expressions in bioinformatics research

Regular expressions are a common feature of contemporary scripting and programming languages, such as Perl and Java, as well as part of conventional database management systems by their incorporation into various dialects of SQL. Bioinformatics researchers encounter problem scenarios in protein sequence analysis that are ideally suited for the application of regular expression algorithms. This paper describes a representative application of regular expressions in this problem domain, and demonstrates how the effective use of regular expressions can serve to facilitate more efficient and more effective bioinformatics research