in reply to Efficient walk/iterate along a string
- Use benchmark to compare different ways of processing.
- Use Devel::NYTProf to determine what portions of your program are slow
- Can you process on clumps of proteins instead of one-by-one?
- Are there alternate algorithmns for the various tasks you need to achieve?
As Occam said: Entia non sunt multiplicanda praeter necessitatem.
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