S. J. Palmer, M. R. Redfern, G. C. Smith and J. P. L. Cox ``Sticky Egyptians: A technique for assembling genes encoding contrained peptides of variable length'', Nucleic Acids Res. 26:11 (1998) 2560-2564
The mathematics concerns enumeration of the arrangements of strings of black and white beads, subject to local constraints (e.g. no more than 6 whites in a row, and similar things). As far as the application is concerned, the beads correspond to amino acids, but no chemistry is required to follow the mathematics.
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