Clay Shirky
Wed, 19 Jan 2000 07:25:10 -0500 (EST)

> c) is there another way? (as Tony Blair would say, a Third Way)

Wouldn't hashing the string in user-specified sizes make the crunching
the time-consuming part and the queries fast? (assuming it gets TIEd
to a database, or is queried on a command-line, that is.)

If you did something like:

   $strand{$nucleotide_group} .= ":$offset";

where $nucleotide_group was anything from 1 to 6 nucleotides, and
offset was the number of positions, you could do things like look for
specific codons at specific offsets, or make a count of the number of
specific codons, or look for dicodon pairs. The position of the
offests would give you the location of the nucleotide group, just like
a regular array, but the total number of offests linked to any given
nucleotide group would also give you information about relative


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