I agree that asking for a list of infinite and still increasing items is always bad idea, but bioinformatics is not even remotely large field, open problems are reduced to standard CS problems and people from time to time show field needs and advancements. I have added "reference-request" tag not to make it stick, but this is how it really works, there are 3 open problems with variants and that is all.
it looks like too-broad, but it isn't really. I do not have any particular attachment to this question, but I think that for those in the field this is not never ending story.
@Evil Hmm. I thought there would definitely be more than 3 open problems there. Perhaps no-one bothered to write them down as 'list of open problems', but I really doubt there are only 3. Perhaps you can get to some point with calling everything a 'variant', but I don't think that's very helpful. I don't get your argument about the size of the field, to be honest. There are plenty of algorithmic problems, a lot probably open, about e.g. pylogenetic trees in bioinformatics.
It also seems on the rise as biologists more frequently run into algorithmic problems.
The fact that the field is small/young but not dead seems to me a reason why we shouldn't answer this question: the answer is likely to be invalidated sooner or later after new open problems appear.
