in reply to simple string comparison for efficiency

Searching this site for recommendations of BioPerl and/or Fasta will likely give you lots of results. For example, Lower-casing Substrings and Iterating Two Files together has a problem very similar to yours and also a solution. Of course, if the "extreme premium on efficiency" you cite will be backed up by an extreme premium of money, you can achieve better results.

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Re^2: simple string comparison for efficiency
by citromatik (Curate) on May 28, 2009 at 21:29 UTC
    Searching this site for recommendations of BioPerl...

    If you are looking for an efficient solution, stay away from BioPerl

    citromatik

[reply]
      To quote from (the Wayback version of) that page:

      Why BioPerl is Fast

      BLAST tiling in C++: development 1 mo. + analysis 5min;
      BLAST tiling in BioPerl: development 2 d + analysis 30min.
      (the reason cited for BioPerl running slowly is their use of inheritance)
[reply]

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