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Means for simultaneous parallel sequence analysis of a large number of biological polymer macromolecules. Apparatus and methods may use fluorescent labels in repetitive chemistry to determine terminal monomers on solid phase immobilized polymers. Reagents which specifically recognize terminal monome

Means for simultaneous parallel sequence analysis of a large number of biological polymer macromolecules. Apparatus and methods may use fluorescent labels in repetitive chemistry to determine terminal monomers on solid phase immobilized polymers. Reagents which specifically recognize terminal monomers are used to label polymers at defined positions on a solid substrate.

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What is claimed is: 1. A method for determining the incorporation of nucleotides comprising: (a) providing a plurality of target template nucleic acids attached to a substrate in positionally separated regions at a density of at least 1000 regions per cm2; (b) hybridizing at least one primer to sai

What is claimed is: 1. A method for determining the incorporation of nucleotides comprising: (a) providing a plurality of target template nucleic acids attached to a substrate in positionally separated regions at a density of at least 1000 regions per cm2; (b) hybridizing at least one primer to said plurality of target template nucleic acids to form hybridized primer; (c) contacting said hybridized primer with, at least one nucleotide and a template-dependent nucleic acid polymerase, wherein said nucleotide comprises a label, under conditions whereby the hybridized primer is elongated by template-directed addition of a nucleotide; and (c) detecting the addition of said nucleotide by detecting the label and thereby determining the incorporation of the nucleotide. 2. The method of claim 1 wherein said primer is complementary to a common priming sequence present in the target template nucleic acids. 3. The method of claim 2 wherein the priming sequence is at the 3' end of the target template nucleic acids. 4. The method of claim 2 wherein the nucleotide further comprises a blocking group that blocks incorporation of additional nucleotides and wherein each of the label and the blocking group are removable and further comprising removing the label and the blocking group following detecting the addition of said nucleotide by detecting the label. 5. The method of claim 4 further comprising repeating steps (b) and (c) following the removal of the label and the blocking group. 6. The method of claim 4 wherein the removal of the label and the blocking group comprises a reaction that removes both the label and the blocking group and further comprising repeating steps (b) and (c) following the removal of the label and the blocking group. 7. A method for polynucleotide analysis comprising: (a) providing a plurality of different target template nucleic acids attached to a support in positionally separated regions at a density of at least 1000 regions per cm2; (b) hybridizing a primer to the target template nucleic acids to obtain a hybridized primer; (c) contacting the hybridized primer with a plurality of species of nucleotides and a template dependentnucleic acid polymerase, wherein the nucleotides comprise a removable label and a removable blocking group and wherein each species of nucleotides comprises a different label that is distinguishable from the label on each of the other species of nucleotides; (d) extending the hybridized primer by incorporation of a nucleotide; (e) scanning the substrate to detect a signal from the label, wherein the signal indicates the species of nucleotide that was incorporated in (d); (f) removing the label and the blocking group; (g) repeating steps (c) to (f) at least once; and (h) determining at least a portion of the sequence of the target template nucleic acid from the species of nucleotide incorporated in step (d). 8. The method of claim 4 wherein the target template nucleic acids are attached to the substrate directly. 9. The method of claim 7 wherein the primer is complementary to a common sequence present in all of the target template nucleic acids. 10. The method of claim 7 wherein the species of nucleotides comprise adenine, guanine, cytosine and thymine. 11. The method of claim 7 wherein step (e) comprises treatment with mild acidic conditions. 12. The method of claim 7 wherein step (e) comprises treatment with mild basic consitions. 13. The method of claim 7 wherein the label and the blocking group are both attached to the nucleotide at the 3' hydroxyl position of the sugar.