Fragmented replicons do not incur CIS interactions at the proper rate

[cerebis]

Intramolecular (cis) interactions should be the most frequently occurring and this is the case for individual genomic sequences.

However, when the provided sequence for a single DNA molecule is fragmented (such as with draft genomes), sim3C will currently not generate interactions between the pieces at the rate for cis interactions. Instead, these are always treated as inter-molecular (trans) interactions.

To deal with this, the model of a community must be expanded to include the notion of a molecule group. Sequences (segments) from the same molecule would then be treated as targets of for site selection when a cis interaction is being generated.

One point to note is that since any intervening sequence and relative orientations cannot be known in these cases, the two sites for such inter-segment events cannot be constrained by the empirical distribution of separation.