Although the validity of many such patents has recently been in doubt, a landmark ruling by the US Federal Court of Appeals last week (Association for Molecular Pathology v. USPTO; the Myriad gene patent litigation) reaffirmed their validity. E.g. http://www.phgfoundation.org/news/9422
To me that sounds like common sense, in the same way one cannot patent "gold", "platinum", or "elephants", even if they are hard to catch or find.
Justice Thomas wrote: “A naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated…It is undisputed that Myriad did not create or alter any of the genetic information encoded in the BRCA1 and BRCA2 genes”.
One view to take is when it comes to bioinformatics and recent changes in the world of gene patents, the ruling has little bearing on the day to day activities of the bioinformatics group. What the ruling does mean is the bioinformatics group/scientist needs to engage the intellectual property group of lawyers and their assistants in order that both sides agree to a strategy to take up work on certain genes or gene sequences.
In other words, the bioinformatics researchers should not act (i.e., engage in decision-making) without having this conversation. Universities, institutes, gov't labs and for-profits all have lawyers to deal with invention disclosures. Make a phone call and start the conversation.
Contributory infringement, [...], usually consists of selling a component of a
patented invention, knowing that the component has no use except in that invention.
So components that have uses other than in that invention might be safe from indirect infringement. This probably makes unintentional infringement of isolated gene patents by generic bioinformatics tools somewhat unlikely.