 A profile HMM is a variant of an HMM relating specifically to biological sequences.Profile HMMs turn a multiple sequence alignment into a position-specific scoring system, which can be used to align sequences and search databases for remotely homologous sequences.They capitalise on the fact that certain positions in a sequence alignment tend to have biases in which residues are most likely to occur, and are likely to differ in their probability of containing an insertion or a deletion.