Detecting pseudoknots and other local base-pairing structures in RNA sequences

The current version of RNAFOLD now has the capability for conducting comparative studies relative to nonbifurcating hairpins contained in the global structures produced by the dynamic programming and Monte Carlo methods. It also has the capability of both finding and comparing hairpins and pseudoknots independently of global structures. The efficacy of these increased capabilities has been tested for select families of sequences, and the results thus far indicate favorable utility. Under consideration is a further extension designed to incorporate pseudoknots within global structures. Written in the C language, RNAFOLD and its companion program, GENALIGN, for doing multiple alignments in the comparison of pseudoknots and hairpins, is available for UNIX systems on standard 1/2-inch, 9-track tape or on SUN tape cartridges.