Is there a methodology for detecting whether a genome has been tampered with by a biologist? For instance, say there has been an ebola outbreak such as in "The Andromeda Strain". Is there a way a researcher can tell by just looking at the ebola genetic data and determine it is a genetically engineered strain?
Some ideas I have:
organism is abnormally close to unrelated organisms, i.e. some of the genetic code from the other organisms has been inserted into the first
subsequences are very different from the rest of the genome. If there is a consistent rate of mutation applied to the entire genome, then a subsequence that is abnormally noise free could be inserted.
combination of 1 and 2: finding clear instances of unrelated organism genomes inserted into the genome being examined.
Additionally, are there any publicly accessible reference genomes that are known to be genetically engineered, that I could use as examples to test such ideas?
UPDATE: the wikipedia article on detecting genetically modified organism is not quite what I am looking for, since it claims current methods cannot detect unknown genetic modification.
Currently, it is highly unlikely that the presence of unexpected or even unknown GMOs will be detected, since either the DNA sequence of the transgene or its product, the protein, must be known for detection.