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Thus, only relative differences between the elements could be reported.
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Network theory helps to describe relationships between every pair of elements, where the elements could be genes, proteins, metabolites, etc.
Only 42 of the elements could be categorized as SVA_A.
It is impossible to use traditional phylogenetic reconstruction methods to infer relationships between Alu elements, as, with their very high copy number, many elements in a young Alu subfamily share a consensus sequence, therefore the relationships between these elements could not be resolved.
Alternatively, the differences observed between the two elements could be due to the existence of differential transposition and regulation mechanisms.
In addition, retention of lubricants at the contact points between the moving elements could be a hurdle for further implementation.
However, the presence of solo-LTR sequences does suggest that recombination between the repeated sequences of the LTR elements could be a contributing factor in the reorganization of Verticillium dahliae genome.
Equally, POTRA candidate sequences were allowed if a short insertion in a loop between the POTRA structural elements could be observed.
In this study, complex non-additive effects of combinations of mutations were observed, and physical interactions between mutated elements could be demonstrated by chromosome conformation capture technology.
Spatial or temporal relationships between linked individual elements could then be further processed and computed (Marcus et al. 1999).
Alternatively, the reciprocal monophyly between the elements of each species could be the consequence of extensive gene conversion between all of the copies of each genome.
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