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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
by hrjet 12y ago
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.
- sakai 12y agoIn principle, some of them can be yes. Though genetic reference datasets tend to be much larger than, e.g., codebases -- and therefore require different approaches. 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)!
- infinite8s 12y agoWouldn't some of the new timeseries motif searching approaches work in this domain (you could assume each codon is a quantized enumerated value). Something like iSax (http://www.cs.ucr.edu/~eamonn/iSAX/iSAX.html http://www.cs.ucr.edu/~eamonn/iSAX/iSAX.html) or Dynamic Time Warping (for motifs that are noisy) - http://www.cs.ucr.edu/~eamonn/SIGKDD_trillion.pdf http://www.cs.ucr.edu/~eamonn/SIGKDD_trillion.pdf