This invention discloses a highly efficient method, system and apparatus for nucleic acid analysis, including sequencing (both automated re-sequencing and de-novo sequencing). The system is capable of sequencing DNA sizes ranging from fragments to mammalian size genomes having mouse draft quality at a much reduced cost. The system comprises a massive parallel capillary electrophoretic separation using two-dimensional monolith multi-capillary arrays (2D-MMCA). Sequence identification can be performed using fluorescent or otherwise labeled dideoxynucleotide-terminated DNA extension product generated by gel matrix-, or beads-, or substrate tethered-, or otherwise immobilized colonies of single template molecules. Cost reduction is a significant advantage over currently known methods because of: (i) using massively parallel sub-nanoliter volume reactions; and (ii) employing 2D-MMCAs that increase the throughput of the CE separation and detection by at least two orders of magnitude compared to the commercial high-throughput DNA machines.