LNCS 2950 - Aspects of Molecular Computing (Frontmatter Pages)

162 Max H. Garzon, Kiranchand V. Bobba, and Bryan P. Hyde
Six large plasmids of lengths varying between 3K and 4.5Kbps were shredded
to fragments of size 40 or less and thrown into a tube containing a basis B of three
different qualities (values of τ) consisting of 36−mers. The first set Nxh consisted
of a set of non-crosshybridizing 40-mers, the length of the longest fragment in
the shredded plasmids x; the second set Randxh was a randomly chosen set of
40-mers; and the third set, a set Mxh of maximally crosshybrizing 40-mer set
consisting of 18 copies of the same strand and 18 copies of its Watson-Crick
complement. The hybridization reactions were determined by the h-distance for
various thresholds τ between 0% and 50% of the basis strand length n, which
varied between n =10, 20, 40. Each experiment was repeated 10 times under
identical conditions. The typical signatures of the six plasmids are illustrated
in Fig. 4, averaged pixelwise for one of them, together with the corresponding
standard deviation of the same. Fig. 5(a) shows the signal-to-noise ratio (SNR) in
effect size units, i.e., given by the pixel signals divided by the standard deviation
for the same plasmid, and Fig. 5(b) shows the chipwise SNR comparison for all
plasmids, in the same scale as shown in Fig. 4.
(a) (b) (c)
Fig. 4. Signatures of a plasmid genome in (a) one run (left); (b) average
over 10 runs; and (c) noise (right, as standard deviation), on a set on noncrosshybridizing
probes.
Examination of these results indicates that the signal obtained from the
Mxh set is the weakest of all, producing results indistinguishable from noise,
certainly due to the random wandering of the molecules in the test tube and their
enountering different base strands (probes.)Thisisinclearcontrastwiththe
signals provided by the other sets, where the noise can be shown to be about 10%
of the entire signal. The random set Randxh shows signals in between, and the
Nxh shows the strongest signal. The conclusion is that, under the assumptions
leading to the definition above, an appropriate base set and a corresponding
hybridization stringency do provide an appropriate definition of the signature of
agivenset.