A versatile divide and conquer technique for optimal string alignment
Common string alignment algorithms such as the basic dynamic programming algorithm (DPA) and the time efficient Ukkonen algorithm use quadratic space to determine an alignment between two strings. In this paper we present a technique that can be applied to these algorithms to obtain an alignment usi...
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| Veröffentlicht in: | Information processing letters 1999-05, Vol.70 (3), p.127-139 |
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| creator | Powell, David R. Allison, Lloyd Dix, Trevor I. |
| description | Common string alignment algorithms such as the basic dynamic programming algorithm (DPA) and the time efficient Ukkonen algorithm use quadratic space to determine an alignment between two strings. In this paper we present a technique that can be applied to these algorithms to obtain an alignment using only linear space, while having little or no effect on the time complexity. This new technique has several advantages over previous methods for determining alignments in linear space, such as: simplicity, the ability to use essentially the same technique when using different cost functions, and the practical advantage of easily being able to trade available memory for running time. |
| doi_str_mv | 10.1016/S0020-0190(99)00053-8 |
| format | Article |
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| ispartof | Information processing letters, 1999-05, Vol.70 (3), p.127-139 |
| issn | 0020-0190 1872-6119 |
| language | eng |
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| source | Elsevier ScienceDirect Journals |
| subjects | Algorithmics. Computability. Computer arithmetics Algorithms Applied sciences Computer science control theory systems Data processing. List processing. Character string processing Dynamic programming Edit distance Exact sciences and technology Information processing Mathematical models Memory organisation. Data processing Sequence alignment Software Studies Theoretical computing |
| title | A versatile divide and conquer technique for optimal string alignment |
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