Patent ID: 7561972

Claim:
A method of designing a polynucleotide sequence that encodes a polypeptide sequence of a predetermined polypeptide, the method comprising: (A) obtaining a frequency lookup table corresponding to an expression system, wherein (i) the frequency lookup table comprises a plurality of sequence elements and a plurality of frequency ranges, (ii) each frequency range in the plurality of frequency ranges is for a corresponding sequence element in the plurality of sequence elements, (iii) each respective frequency range in the plurality of frequency ranges specifies a range of relative frequencies with which the sequence element corresponding to the respective frequency range can occur in a polynucleotide that is to be expressed in the expression system, and (iv) each respective sequence element in the plurality of sequence elements optionally includes a frame designation which defines the frame of the respective sequence element relative to the reading frame of said predetermined polypeptide; (B) defining, on a suitably programmed computer, the polynucleotide sequence using the frequency lookup table, wherein the defining comprises, for each respective sequence element in the frequency lookup table, determining whether the respective sequence element encodes a portion of the polypeptide sequence in the frame designation specified for the respective sequence element when there is a frame designation for the respective sequence element in the frequency lookup table; determining whether the respective sequence element encodes a portion of the polypeptide sequence in any frame when there is no frame designation for the respective sequence element in the frequency lookup table; wherein, when the respective sequence element encodes a portion of the polypeptide sequence, the sequence element is incorporated into the polynucleotide at a frequency of occurrence that is within the frequency range specified for the respective sequence element in the frequency lookup table, and wherein the frequency lookup table comprises at least two different sequence elements that each encode a portion of the polypeptide sequence in a frame designation specified for the at least two different sequence elements; and (C) outputting the polynucleotide sequence to a user interface device, a tangible computer readable storage medium; or displaying the polynucleotide sequence in user readable form.