1. A method for optimizing a gene sequence for expression of a protein in a host cell, the method comprising: (a) identifying a plurality of sequence factors that affect the expression of the protein in the host cell; (b) defining a particle swarm optimization algorithm comprising a function for each of the plurality of sequence factors; and (c) applying the particle swarm optimization algorithm to the gene sequence to obtain an optimized gene sequence for expression of the protein in the host cell, wherein the optimized gene sequence takes into account of the plurality of sequence factors and achieves the maximum value of the swarm optimization algorithm, wherein at least the applying step is performed on a computer.