how does RE# find the leftmost-longest match efficiently? remember the bidirectional scanning we mentioned earlier - run the DFA right to left to find all possible match starts, then run a reversed DFA left to right to find the ends. the leftmost start paired with the rightmost end gives you leftmost-longest. two linear DFA scans, no backtracking, no ambiguity.
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The first such method was developed in biophysicist Steve Quake’s lab at Caltech and commercialized by Helicos Biosciences, but became unavailable after the company declared bankruptcy, saddled by legal issues and unable to find a market niche. These days, the canonical technique comes from a company called Pacific Biosciences (PacBio). Scientists often refer to single-molecule techniques as “third-generation” DNA sequencing, though they’re often also lumped into the NGS bucket with Illumina.
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