Dynamic programming solutions to a number of different recurrence equations for sequence comparison and for RNA secondary structure prediction are considered. These recurrences are defined over a number of points that is quadratic in the input size; however only a sparse set matters for the result. Efficient algorithms for these problems are given, when the weight functions used in the recurrences are taken to be linear. The time complexity of the algorithms depends almost linearly on the number of points that need to be considered; when the problems are sparse this results in a substantial speed-up over known algorithms.

Sparse dynamic programming I: linear cost functions / Eppstein, D; Galil, Z; Giancarlo, R; Italiano, G. - In: JOURNAL OF THE ASSOCIATION FOR COMPUTING MACHINERY. - ISSN 0004-5411. - 39:3(1992), pp. 519-545. [10.1145/146637.146650]

Sparse dynamic programming I: linear cost functions

Italiano G
1992

Abstract

Dynamic programming solutions to a number of different recurrence equations for sequence comparison and for RNA secondary structure prediction are considered. These recurrences are defined over a number of points that is quadratic in the input size; however only a sparse set matters for the result. Efficient algorithms for these problems are given, when the weight functions used in the recurrences are taken to be linear. The time complexity of the algorithms depends almost linearly on the number of points that need to be considered; when the problems are sparse this results in a substantial speed-up over known algorithms.
File in questo prodotto:
Non ci sono file associati a questo prodotto.
Pubblicazioni consigliate

Caricamento pubblicazioni consigliate

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11385/199851
Citazioni
  • Scopus 104
  • ???jsp.display-item.citation.isi??? 78
social impact