Once upon a time, I had briefly looked at gene matching algorithms like FASTA. n00b question: Can these algorithms be generalized to any code (not just genetic codes). For example, to match Java bytecode, or x86 op-codes.
One of the core things we're working on is a data structure for more efficient, constant-time sequence lookups, and we've definitely thought of some non-bioinformatics use cases as well. Happy to answer any more specific questions by email too (in my profile)!