## Efficient Algorithms for Sequence Analysis (1991)

Venue: | Proc. Second Workshop on Sequences: Combinatorics, Compression. Securiry |

Citations: | 1 - 0 self |

### BibTeX

@INPROCEEDINGS{Eppstein91efficientalgorithms,

author = {David Eppstein and Zvi Galil and Raffaele Giancarlo and Giuseppe F. Italiano},

title = {Efficient Algorithms for Sequence Analysis},

booktitle = {Proc. Second Workshop on Sequences: Combinatorics, Compression. Securiry},

year = {1991},

pages = {17--21}

}

### OpenURL

### Abstract

: We consider new algorithms for the solution of many dynamic programming recurrences for sequence comparison and for RNA secondary structure prediction. The techniques upon which the algorithms are based e#ectively exploit the physical constraints of the problem to derive more e#cient methods for sequence analysis. 1. INTRODUCTION In this paper we consider algorithms for two problems in sequence analysis. The first problem is sequence alignment, and the second is the prediction of RNA structure. Although the two problems seem quite di#erent from each other, their solutions share a common structure, which can be expressed as a system of dynamic programming recurrence equations. These equations also can be applied to other problems, including text formatting and data storage optimization. We use a number of well motivated assumptions about the problems in order to provide e#cient algorithms. The primary assumption is that of concavity or convexity. The recurrence relations for bo...