Nucleic Acids Res 12: 45-52 (1984)
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.
Mesh Headings