Researchers are becoming increasingly concerned that the confidentiality of their novel biomolecule sequences is being jeopardised, particularly when these sequences are either submitted to sequence databases or uploaded as query terms onto internet-based bioinformatic software suites. The researcher’s fears stem from the fact that the actual uploading of their sequences acts as a novelty destroying prior disclosure or publication, and that this may subsequently preclude valid patent protection for the sequences. This article addresses the key issues involved in the analyses of biomolecules, highlighting potential risks taken by many researchers in regard to patent protection and suggests possible ways in which these risks may be mitigated.