Impact of genome assembly status on ChIP-Seq and ChIP-PET data mapping.
BACKGROUND
ChIP-Seq and ChIP-PET can potentially be used with any genome for genome wide profiling of protein-DNA interaction sites. Unfortunately, it is probable that most genome assemblies will never reach the quality of the human genome assembly. Therefore, it remains to be determined whether ChIP-Seq and ChIP-PET are practicable with genome sequences other than a few (e.g. human and mouse).


RESULTS
Here, we used in silico simulations to assess the impact of completeness or fragmentation of genome assemblies on ChIP-Seq and ChIP-PET data mapping.


CONCLUSIONS
Most currently published genome assemblies are suitable for mapping the short sequence tags produced by ChIP-Seq or ChIP-PET.
Buisine
Nicolas
N
Department Evolution des Régulation Endocriniennes, Museum National d'Histoire Naturelle, 7, Rue Cuvier, 75231 Paris Cedex 05, France.
Sachs
Laurent
L