(Neil's not here ? yessss ;-) ).Yes, MongoDB is a key Value DataStore, so, for example, if you want to save a pair (name,sequence), then it is straightforward with mongodb
and you can also add some indexed data:
However I'm not sure it would a good way to store some large sequences.
If you really want to use a key/value datastore, have a look at BerkeleyDB. This (free) engine is interesting because it is fast (everything is binary data), it can be embedded (no network involbed) and you can ask for only retrieving a chunk of your value. So, say, if you store the human chr1 and ask for the very first bases, you won't have to load the entire chromosome in memory.