Improved algorithms for searching restriction maps

W. Miller, J. Barr, K. E. Rudd

Research output: Contribution to journalArticle

6 Scopus citations


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.

Original languageEnglish
Pages (from-to)447-456
Number of pages10
JournalComputer Applications in the Biosciences
Issue number4
StatePublished - Jan 1 1991
Externally publishedYes


ASJC Scopus subject areas

  • Medicine (miscellaneous)
  • Molecular Biology
  • Statistics and Probability
  • Computational Mathematics
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Biochemistry

Cite this

Miller, W., Barr, J., & Rudd, K. E. (1991). Improved algorithms for searching restriction maps. Computer Applications in the Biosciences, 7(4), 447-456.