### Abstract

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(MP^{3}) time and O(M + p^{2}) 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 language | English |
---|---|

Pages (from-to) | 447-456 |

Number of pages | 10 |

Journal | Computer Applications in the Biosciences |

Volume | 7 |

Issue number | 4 |

State | Published - Jan 1 1991 |

Externally published | Yes |

### Fingerprint

### ASJC Scopus subject areas

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

### Cite this

*Computer Applications in the Biosciences*,

*7*(4), 447-456.

**Improved algorithms for searching restriction maps.** / Miller, W.; Barr, J.; Rudd, K. E.

Research output: Contribution to journal › Article

*Computer Applications in the Biosciences*, vol. 7, no. 4, pp. 447-456.

}

TY - JOUR

T1 - Improved algorithms for searching restriction maps

AU - Miller, W.

AU - Barr, J.

AU - Rudd, K. E.

PY - 1991/1/1

Y1 - 1991/1/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=0026095420&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0026095420&partnerID=8YFLogxK

M3 - Article

C2 - 1747775

AN - SCOPUS:0026095420

VL - 7

SP - 447

EP - 456

JO - Bioinformatics (Oxford, England)

JF - Bioinformatics (Oxford, England)

SN - 1367-4803

IS - 4

ER -