  Multiple sequence alignment (MSA) is a fundamental algorithm in
bioinformatics. In a situation when the alignment might need to be protected
while revealing the other information such the input sequences and the
alignment score, zero knowledge proof can be used. In this paper, a validator
checks the consistency between the input sequence and the alignment, and
between the alignment and the alignment score. The validator is written in
Circom language which will be compile into a circuit. Using a zero knowledge
prove system called zkSNARK, a cryptographic proof is generates for the circuit
and its input. This proof demonstrates that all inputs are consistent without
revealing the actual alignment.
