Methods for sorting polynucleotides using oligonucleotide tags

A method for determining the nucleotide sequence of a target polynucleotide, the method comprising the steps of:

• generating from the target polynucleotide a plurality of fragments that cover the target polynucleotide;
• attaching an oligonucleotide tag from a repertoire of tags to each fragment of the plurality (i) such that substantially all different fragments have different oligonucleotide tags attached and (ii) such that each oligonucleotide tag from the repertoire comprises a plurality of subunits and each subunit of the plurality consists of an oligonucleotide having a length from three to six nucleotides or from three to six basepairs, the subunits being selected from a minimally cross-hybridizing set, wherein a subunit of the set and a complement of any other subunit of the set would have at least two mismatches;
• sorting the fragments by specifically hybridizing the oligonucleotide tags with their respective complements, the respective complements being attached as uniform populations of substantially identical complements in spatially discrete regions on one or more solid phase supports;
• determining the nucleotide sequence of a portion of each of the fragments of the plurality;
• and
• determining the nucleotide sequence of the target polynucleotide by collating the sequences of the fragments.

A method of identifying a population of mRNA molecules, the method comprising the steps of:

• forming a population of cDNA molecules from the population of mRNA molecules, the cDNA molecules being complementary to the mRNA molecules and each cDNA molecule having an oligonucleotide tag attached, (i) such that substantially all different cDNA molecules have different oligonucleotide tags attached and (ii) such that each oligonucleotide tag comprises a plurality of subunits and each subunit of the plurality consists of an oligonucleotide having a length from three to six nucleotides, the subunits being selected from a minimally cross-hybridizing set, wherein a subunit of the set and a complement of any other subunit of the set would have at least two mismatches;
• sorting the cDNA molecules by specifically hybridizing the oligonucleotide tags with their respective complements, the respective complements being attached as uniform populations of substantially identical complements in spatially discrete regions on one or more solid phase supports;
• determining the nucleotide sequence of a portion of each of the sorted cDNA molecules;
• and
• identifying the population of mRNA molecules by the frequency distribution of the portions of sequences of the cDNA molecules.