Some simple computational methods to improve the folding of large RNAs

Abstract

Computational methods are described which increase the efficiency of the RNA folding algorithm described by Zuker and Stiegler. Bit addressing has been used to reduce the memory requirements from 2NxN to NxN/2. The order in which the nucleotide sequence is examined internally has been altered, and some additional short arrays which carry temporary information have been introduced. These changes optimize the management of the large data arrays generated by the algorithm. The methods were developed for use with a UNIVAC 1100/82 computer. They are, however, easily adaptable to other computers; especially those with virtual memory capabilities. The analysis of sequences up to 1000 nucleotides long are relatively routine, and larger searches are also feasible. Some limitations and applications of the algorithm are also discussed.