The conditions under which oligonucleotide probes hybridize preferentially
with entirely complementary and homologous nucleic acid targets are
described. Using these hybridization conditions, overlapping
oligonucleotide probes associate with a target nucleic acid. Following
washes, positive hybridization signals are used to assemble the sequence
of a given nucleic acid fragment. Representative target nucleic acids are
applied as dots. Up to to 100,000 probes of the type
(A,T,C,G)(A,T,C,G)NB(A,T,C,G) are used to determine sequence information
by simultaneous hybridization with nucleic acid molecules bound to a
filter. Additional hybridization conditions are provided that allow
stringent hybridization of 6 10 nucleotide long oligomers which extends
the utility of the invention. A computer process determines the
information sequence of the target nucleic acid which can include targets
with the complexity of mammalian genomes. Sequence generation can be
obtained for a large complex mammalian genome in a single process.