The described method provides, methods, and kits to produce, identify,
catalog and classify a comprehensive collection of nucleic acid targets
produced from a nucleic acid sample. The method, referred to as
Cataloging and Classification of Sequence Tags, involves generating a set
of target nucleic acid fragments; coupling the target nucleic acid
fragments to a nucleic acid bridge comprising, for example, two or more
primer binding sites and two recognition sites for cleavage at a site
offset from the recognition site to the fragment's end; and cleaving the
fragments to generate chimeric nucleic acids of known length. The nucleic
acid bridge is thus disposed between the two nucleic acid fragments in
the chimeric nucleic acid. The resulting duplex nucleic acids comprise a
set of sequence tags (i.e., by amplification using universal primers),
comprising an addressable portion, a target nucleic portion and a portion
of the nucleic acid bridge. Single-stranded or partial duplex sequence
tags may be captured by coupling to a complementary capture probe.
Capture probe-sequence tag hybrids, may be detected employing a labeled
detector probe. The method allows a complex sample of nucleic acids to be
cataloged in a reproducible and sequence-specific manner. The method
further provides methods for analysis of the above sample to classify the
sequence tags; determine the presence and relative amounts of sequences
of interest; derive expressed genes signatures and differential gene
expression signatures; and identify putative expressed sequence tags
(EST).