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    $\begingroup$ As for me, the phrase a transmembrane protein that is supposed to selectively filter K ions contains an amino acid sequence "TVGYG" in this site is worth a +1. $\endgroup$ Commented May 27, 2012 at 22:45
  • $\begingroup$ The syntax information on the function's doc page clearly lists its arguments as strings, not patterns. If your question really only is "Is it naive to expect more functionality or am I too demanding on Mathematica?" I'm afraid I have to vote to close it as either "not constructive" or "not a real question". $\endgroup$ Commented May 27, 2012 at 22:52
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    $\begingroup$ If you could rephrase your question to something like "how can I mimic the dreamed behavior of SequenceAlignment["A", Alternatives["A", "B"]]?" then I think you should be OK. Otherwise, your question doesn't adhere to the rules as delineated in the FAQ. $\endgroup$ Commented May 27, 2012 at 23:07
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    $\begingroup$ "BLAST" is specifically listed as a permissible value for the SimilarityRules option for SequenceAlignment. Perhaps it might be what you are looking for? $\endgroup$ Commented May 27, 2012 at 23:54
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    $\begingroup$ @WReach The SimilarityRules option specifies how acceptable a candidate candidate character is for matching another. In mma "BLAST" seems to me just the name of a specific square table, it did not help aligning a pattern. you might browse <en.wikipedia.org/wiki/BLAST> $\endgroup$ Commented May 28, 2012 at 4:49