Abstract: A method of retrieving a subset of polynucleotide molecules from a mixture of polynucleotide molecules includes receiving a mixture of nucleotide sequences comprising one or more polynucleotide molecules, synthesizing one or more identifier (ID) regions onto the one or more polynucleotide molecules, and sequencing members of the population of polynucleotide molecules to associate the sequence of one or more of the molecules (the “Polynucleotide Sequence”) with the sequence of the attached ID region (the “ID Sequence”). The method also includes generating a bead-bound library of one or more beads comprising subsets of identical polynucleotide molecules. Each bead is identified by the ID Sequence of the associated Polynucleotide Sequence.