Methods of sequencing nucleic acid molecules

A method for nucleic acid sequence identification, comprising:

• (a) providing a plurality of nucleic acid molecules immobilized at a detection area, wherein said plurality of nucleic acid molecules has sequence homology with a template nucleic acid molecule;
• (b) bringing said plurality of nucleic acid molecules in contact with a first reaction mixture comprising a first plurality of nucleotides, under conditions sufficient to incorporate first nucleotides of said first plurality of nucleotides into a first subset of a plurality of sequences hybridized to said plurality of nucleic acid molecules,
• wherein at least a subset of said first plurality of nucleotides is labeled, wherein said first reaction mixture comprises nucleotides of at most three canonical base types;
• (c) subsequent to (b), bringing said plurality of nucleic acid molecules in contact with a second reaction mixture comprising a second plurality of nucleotides that are of a same canonical base type as said first plurality of nucleotides, under conditions sufficient to incorporate second nucleotides of said second plurality of nucleotides into a second subset of said plurality of sequences,
• wherein no intervening nucleotide is provided to said plurality of nucleic acid molecules between (b) and (c), under conditions sufficient to incorporate said intervening nucleotide into said plurality of sequences;
• and
• (d) using signals detected from said detection area that correspond to at least said first nucleotides incorporated into said first subset of said plurality of sequences to identify one or more nucleic acid bases of said plurality of nucleic acid molecules.