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Speeding up Dynamic Programming with Application to the Computation of RNA Structure

David Eppstein; Zvi Galil; Raffaele Giancarlo

Title:
Speeding up Dynamic Programming with Application to the Computation of RNA Structure
Author(s):
Eppstein, David
Galil, Zvi
Giancarlo, Raffaele
Date:
Type:
Technical reports
Department:
Computer Science
Permanent URL:
Series:
Columbia University Computer Science Technical Reports
Part Number:
CUCS-327-88
Abstract:
We describe the solution of a two dimensional recurrence used to compute the secondary structure of RNA. A naive dynamic programming solution to this recurrence takes time O (n4); this time had previously been improved to O (n3). Our new algorithm makes use of the convexity of the energy functions for RNA secondary structure to reduce the time to O(n2 1og2 n). When the energy function is modeled by logarithms or other simple functions we solve the recurrence in time O(n2Iognloglogn). Our algorithms are simple and practical.
Subject(s):
Computer science
Item views:
278
Metadata:
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