When there are more than one chromosome under consideration, the method is similar by modeling the chromosomes one by one.
One of these models, which we will study in this paper, models the chromosomes of a genome with paths and cycles in a graph.
Thus these assemblies represent a model for the chromosomes of T. cruzi, and, though they are still incomplete, they are a vast improvement on what was previously available.
The importance of chromosomal domain structure in dictating silencing efficiency was further supported by modelling the chromosome 3 dataset.
Distributions of the number of gene models along the chromosomes of the annotation presented here and the previous JGI annotation are shown in Figure S1.
Here we introduce a novel mouse model, the Sex Chromosome Trisomy model, which compares XXY, XYY, XY, and XX mice within litters.
In this model, the Y chromosome (or its equivalent in other sex-determination systems) would encode an endonuclease that cuts and destroys the X chromosome during male meiosis, thereby ensuring that most viable sperm contain a Y chromosome (Newton et al., 1976; Wood and Newton, 1991; Windbichler et al., 2007, 2008; Galizi et al., 2014).
While a coarse-grained model of the chromosome is employed here, a mapping to physical units can be conducted using results from fluorescence in situ hybridization (FISH) experiments [19].
In addition, all of the factors in the model, including the chromosome main effects, are statistically significant.
Further discuss about the parameterization will appear below in our response to a comment from Reviewer 3. Secondly, the meaning of "chromosome [that] would be much longer than individual [ribozyme] genes" should be understood as in respect of the relative length, e.g., in the model here, the chromosome is four times as long as individual ribozymes.
