Elsevier

Methods in Enzymology

Volume 183, 1990, Pages 281-306
Methods in Enzymology

[17] Predicting optimal and suboptimal secondary structure for RNA

https://doi.org/10.1016/0076-6879(90)83019-6Get rights and content

Publisher Summary

There are two methods of predicting secondary structure: phylogeny and energy minimization. Phylogeny relies on alignment and subsequent folding of several sequences into similar structures for functionally analogous RNA. Energy minimization relies on thermodynamic parameters and computer. There are two versions of the program: LRNA folds linear sequences, and CRNA folds circular sequences. LRNA and CRNA have the same user interface. Information about the structure helps the program fold the sequence into a better secondary structure. The locations of single-stranded sites, double-stranded sites, or known helixes are easily entered in LRNA. In batch mode, a sequence of commands in a batch file is run non-interactively, usually in nonprime time. The user can type in the batch file using an editor or the interactive program BATGEN. BATGEN first asks for the batch file name and the header file name. The header file contains information placed at the top of the batch file, such as a system command to change directories.

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