Please note that the content of this book primarily consists of articles available from Wikipedia or other free sources online. The Nucleic Acid Package, is a growing software suite for the analysis and design of nucleic acid systems . Jobs can be run online on the NUPACK webserver or NUPACK source code can be downloaded and compiled locally. NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble. The secondary structure of multiple interacting strands is defined by a list of base pairs . A polymer graph for a secondary structure can be constructed by ordering the strands around a circle, drawing the backbones in succession from 5' to 3' around the circumference with a nick between each strand, and drawing straight lines connecting paired bases.

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