## Optimal alignments in linear space (1988)

Venue: | CABIOS |

Citations: | 206 - 3 self |

### BibTeX

@ARTICLE{Myers88optimalalignments,

author = {Eugene W. Myers and Webb Miller},

title = {Optimal alignments in linear space},

journal = {CABIOS},

year = {1988},

volume = {4},

pages = {11--17}

}

### Years of Citing Articles

### OpenURL

### Abstract

Space, not time, is often the limiting factor when computing optimal sequence alignments, and a number of recent papers in the biology literature have proposed space-saving strategies. However, a 1975 computer science paper by Hirschberg presented a method that is superior to the newer proposals, both in theory and in practice. The goal of this note is to give Hirschberg’s idea the visibility it deserves by developing a linear-space version of Gotoh’s algorithm, which accommodates affine gap penalties. A portable C-software package implementing this algorithm is available on the BIONET free of charge.

### Citations

712 |
An extension of the string-to-string correction problem
- Lowrance, Wagner
- 1975
(Show Context)
Citation Context ...sitive, can be determined by comparison with a ‘‘standard’’ program. We chose the following straightforward implementation of the classic dynamic programming algorithm for the case where gap(k) = hk (=-=Wagner and Fischer, 1974-=-). To facilitate comparative testing, the procedure arguments match the software interface described below. Our linear-space software’s execution time exceeds that of the simple program by the factor ... |

430 | An improved algorithm for matching biological sequences - Gotoh - 1982 |

198 |
Algorithms for approximate string matching
- Ukkonen
- 1985
(Show Context)
Citation Context ...), whose cost-only version needs O(MN) space. In practice, employing the strategy at most doubles the time and space requirements of the cost-only version. Indeed, with greedy methods (Fickett, 1984; =-=Ukkonen, 1985-=-, Section 3; Miller and Myers, 1985; Myers, 1986), the midpoint computation is twice as efficient as a onepass cost-only computation, implying that the time overhead of the divide-and-conquer approach... |

183 |
A faster algorithm computing string edit distances
- Masek, Paterson
- 1980
(Show Context)
Citation Context ...ion with identical asymptotic time and space complexities. When applied to certain other alignment algorithms, the space requirement becomes sublinear (Myers, 1986), linear (Wagner and Fischer, 1974; =-=Masek and Paterson, 1980-=-), or linear in expectation (Miller and Myers, 1988). Occasionally, the variation is not space-efficient, as with the method of Waterman, Smith, and Beyer (1976), whose cost-only version needs O(MN) s... |

174 | An O(ND) difference algorithm and its variations
- Myers
- 1986
(Show Context)
Citation Context ... algorithms yield an alignment-delivering variation with identical asymptotic time and space complexities. When applied to certain other alignment algorithms, the space requirement becomes sublinear (=-=Myers, 1986-=-), linear (Wagner and Fischer, 1974; Masek and Paterson, 1980), or linear in expectation (Miller and Myers, 1988). Occasionally, the variation is not space-efficient, as with the method of Waterman, S... |

68 |
Sequence comparison with concave weighting functions
- Miller, Myers
- 1988
(Show Context)
Citation Context ...atively simple method yields a simple and novel development that we hope will bring Hirschberg’s idea to a wider audience. Moreover, for affine indel costs, the more general concave-weights software (=-=Miller and Myers, 1988-=-) runs 3.0 times slower and uses 3.5 times more space than the program described in this paper. System and Methods C software implementing the algorithm was written and tested on a Vax 11/780 running ... |

65 | A le comparison program
- Miller, Myers
- 1985
(Show Context)
Citation Context ... needs O(MN) space. In practice, employing the strategy at most doubles the time and space requirements of the cost-only version. Indeed, with greedy methods (Fickett, 1984; Ukkonen, 1985, Section 3; =-=Miller and Myers, 1985-=-; Myers, 1986), the midpoint computation is twice as efficient as a onepass cost-only computation, implying that the time overhead of the divide-and-conquer approach is negligible. Acknowledgment Step... |

54 |
Optimal sequence alignment using affine gap costs
- Altschul, Erickson
- 1986
(Show Context)
Citation Context ...mum cost, then straightforward implementations need O(MN) space. In practice, this space requirement often limits the method’s applicability, and several papers (Taylor, 1984; Watanabe, et al., 1985; =-=Altschul and Erickson, 1986-=-; Gotoh, 1986; Gotoh, 1987) have presented strategies that reduce space consumption by constant factors. These papers fail to note that Hirschberg (1975) showed how to produce an optimal conversion or... |

33 |
Comparative biosequence metrics
- SMITH, WATERMAN, et al.
- 1981
(Show Context)
Citation Context ...ry k-symbol gap. This formulation is converted to a difference problem by the transformations w(a, b) = σ max − σ(a, b) for all pairs (a, b) g = q h = r + 1 ⁄ 2σ max where σ max = max (a, b) σ(a, b) (=-=Smith, et al., 1981-=-). Thus, to produce an alignment that maximizes the similarity score, first apply these transformations and then run the program described in this paper with the resulting w, g, and h. If the minimum ... |

29 | A dynamic programming algorithm to find all solutions in a neighborhood of the optimum
- Waterman, Byers
- 1985
(Show Context)
Citation Context ...e insignificant to the user. Moreover, when one is searching for a particular ‘‘biologically meaningful’’ arrangement, it may be necessary to consider slightly sub-optimal alignments (Waterman, 1983; =-=Waterman and Byers, 1985-=-). One alternative to explicitly constructing all optimal alignments is to modify our linear-space program to produce ‘‘left-most’’ and ‘‘right-most’’ optimal alignments that delineate the range of po... |

21 | A linear space algorithm for computing longest common subsequences - Hirschberg - 1975 |

20 |
Sequence alignments in the neighborhood of the optimum with general application to dynamic programming
- Waterman
- 1983
(Show Context)
Citation Context ...e differences are insignificant to the user. Moreover, when one is searching for a particular ‘‘biologically meaningful’’ arrangement, it may be necessary to consider slightly sub-optimal alignments (=-=Waterman, 1983-=-; Waterman and Byers, 1985). One alternative to explicitly constructing all optimal alignments is to modify our linear-space program to produce ‘‘left-most’’ and ‘‘right-most’’ optimal alignments that... |

17 |
Fast optimal alignment
- Fickett
- 1984
(Show Context)
Citation Context ...and Beyer (1976), whose cost-only version needs O(MN) space. In practice, employing the strategy at most doubles the time and space requirements of the cost-only version. Indeed, with greedy methods (=-=Fickett, 1984-=-; Ukkonen, 1985, Section 3; Miller and Myers, 1985; Myers, 1986), the midpoint computation is twice as efficient as a onepass cost-only computation, implying that the time overhead of the divide-and-c... |

17 |
Alignment of three biological sequences with an efficient traceback
- Gotoh
- 1986
(Show Context)
Citation Context ...d implementations need O(MN) space. In practice, this space requirement often limits the method’s applicability, and several papers (Taylor, 1984; Watanabe, et al., 1985; Altschul and Erickson, 1986; =-=Gotoh, 1986-=-; Gotoh, 1987) have presented strategies that reduce space consumption by constant factors. These papers fail to note that Hirschberg (1975) showed how to produce an optimal conversion or alignment in... |

8 |
Pattern matching of biological sequences with limited storage
- Gotoh
- 1987
(Show Context)
Citation Context ...ions need O(MN) space. In practice, this space requirement often limits the method’s applicability, and several papers (Taylor, 1984; Watanabe, et al., 1985; Altschul and Erickson, 1986; Gotoh, 1986; =-=Gotoh, 1987-=-) have presented strategies that reduce space consumption by constant factors. These papers fail to note that Hirschberg (1975) showed how to produce an optimal conversion or alignment in O(N) space. ... |

3 |
Optimal alignments of biological sequences on a microcomputer
- Watanabe, Urano, et al.
- 1985
(Show Context)
Citation Context ...ark, PA 16802 - 1 -sminimum cost, then straightforward implementations need O(MN) space. In practice, this space requirement often limits the method’s applicability, and several papers (Taylor, 1984; =-=Watanabe, et al., 1985-=-; Altschul and Erickson, 1986; Gotoh, 1986; Gotoh, 1987) have presented strategies that reduce space consumption by constant factors. These papers fail to note that Hirschberg (1975) showed how to pro... |