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© IRL Press

Improved algorithms for searching restriction maps

Webb Miller , John Barr and Kenneth E. Rudd 1

Department of Computer Science, The Pennsylvania State University University Park, PA 16802
1National Center for Biotechnology Information, National Library of Medicine NIH, Bethesda, MD 20894, USA

We present algorithms for searching a DNA restriction enzyme map for a region that best matches a shorter ‘probe’ map. Our algorithms utilize a new model of map alignments, and extensive experiments prove our model superior to earlier approaches for certain applications. Let M be the number of map sites and P be the number of probe sites. Our first algorithm, which optimizes only over a restricted class of alignments, requires O(MP log P) worst-case time and O(M + P) space. Our second algorithm, which optimizes over all alignments, runs in O(MP3) time and O(M + P2) space, under reasonable assumptions about the distribution of restriction enzyme cleavage sites. Combining the algorithms gives a map-searching method that optimizes over all alignments in O(MP log P) time in practice. The algorithms' effectiveness is illustrated by searches involving a genomic restriction map of Escherichia coli.

Received on October 23, 1990; accepted on February 17, 1991

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