Join functions about joining units

DNA polymerase III is actually a complex of seven different sub-units, ranging in length from about 300 to about 1,100 amino acid residues. Only one of the subunits does the actual chemical joining of nucleotides the other subunits are involved in critical accessory functions. For instance, the polymerizing subunit tends to fall off the template DNA after joining only ten to fifteen nucleotides. If this happened in the cell the polymerase would have to hop back on hundreds of thousands of times before replication was complete, slowing replication enormously. However, the complete Pol III—with all seven sub-units—does not fall off until the entire template DNA (which can be more than a million base pairs long) is copied. 

The purpose of the join function is to tell us how well two units will join together when concatenated. In most approaches this function returns a cost, such that we usually talk about join costs. Other formulations are however possible, including the join classifier, which returns true or false, and the join probability, which returns the probability that two units will be found in sequence. 

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