Biomedical Engineering Reference
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associative search queries within the above described synthetic DNA databases.
Associative search queries were executed by hybridization of a database DNA
strand with a complementary query strand. Discrimination in annealing experi-
ments was enhanced by the library design, which guaranteed a minimum Ham-
ming distance between distinct sequences. In their initial annealing experiments
for processing associative search queries, they employed fluorescently labeled
query strands and then performed separation of fluorescent versus nonfluores-
cent beads by Fluorescence-Activated Cell Sorting (FACS). They also experi-
mentally tested variants of conventional PCR techniques for executing
associative search queries, and, in addition, developed a PCR technique for as-
sociative search in the pairwise constructed DNA database.
3.8.3. Analysis of Associative Search
Similar error analysis and experimental testing methods can be employed in
our proposed generalizations of this prior work (55) to tagged genomic DNA. It
would be informative to measure rates of various search errors including: false
positives from near-neighbor mismatches, partial matches, and nonspecific bind-
ing, as well as false negatives from limit-of-detection problems. It is desirable to
directly measure the limits of detection, and to measure the ability to retrieve
rare sequences within databases of high strand diversity.
3.9. Logical Query Processing in Biomolecular Databases
Biochemical operations can be used to execute query operations on this
Biomolecular Database, so as to retrieve subsets of the Biomolecular Database.
Each of the information strands of the database encodes a sequence of data val-
ues v 1 , v 2 , ..., v k , where the i th value v i ranges over a small finite domain D i (e.g.,
D i typically would range over 10 or less possible values, each encoded by a dis-
tinct fixed-length DNA sequence). Retrieval can be specified by logical queries
on the tags of the database as well as associative queries on the attached ge-
nomic DNA strands. The associative searches can be executed by recombinant
DNA operations, for example, variants of PCR combined with surface-
chemistry methods and/or solution-based methods. The logical queries include
the following: (i) SELECTION—selects DNA strands of a given ID or cell type;
and (ii) Logical SELECTION—executes logical queries that select those ge-
nomic DNA strands whose information strands satisfy a specified logical query
formula, whose logical conjunctives include AND as well as OR. These logical
conjunctives are applied to selective predicates of the form "Tag( i ) = v ", where
Tag( i ) is the i th portion of the information tag of a DNA strand of the database,
and v is a fixed value over the domain D i . (The Boolean NOT of a selective
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