This makes possible simultaneous pattern matching on both sense and anti-sense strands of a query sequence. In principle, one could do such a search more inefficiently by testing ainst both sense and anti-sense versions of a sequence. Only one regexp is executed. Regexp patterns are typically much smaller than sequences.
Patterns can be quite complex and it is often difficult to generate the reverse complement pattern.
The Bioperl SeqPattern.pm addresses this problem, providing a convenient set of tools for working with biological sequence regular expressions. Not all patterns have been tested. X Any amino acid . Any amino acid Multiple Format Support Ultimately, this module should be able to build SeqPattern.pm objects objects using a variety of pattern formats such as ProSite, Blocks, Prints, GCG, etc. Currently, this module only supports patterns using a grep-like syntax.