It looks to me that all you need is the standard Needleman-Wunsch algorithm: apply it n times to align your query sequence against all the sequences in $hash, read off the sequence whose best alignment has the longest gap, and then use NW again to align this maximal-gap sequence against the remaining n-1 sequences in $hash.

the lowliest monk

In reply to Re: Simple String Alignment by tlm
in thread Simple String Alignment by monkfan

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