Biomedical Engineering Reference
In-Depth Information
Figure 3
. Predicted functional RNA structures in the genome of Hepatitis B virus. The func-
tion of the F, F
'
, and B elements of the HPRE region have been determined experimentally. The
prediction suggests several new conserved structures with unknown function. In the "mountain
representation" each base pair (
i
,
j
) is represented by a bar from
i
to
j
. The thickness of the bar
indicates its probability or the reliability of the prediction. A color scheme can be used to indi-
cate sequence covariations. Hue encodes the number of compensatory and consistent muta-
tions, while reduced saturation indicates that a small number of sequences is inconsistent with
the structure.
system via innate immune receptors. RNA structure thus receives increased at-
tention in molecular medicine.
A comprehensive understanding of the biology of a cell will ultimately re-
quire the knowledge of all encoded RNAs, the molecules with which they inter-
act, and the molecular structures of these complexes (18). Various approaches to
surveying genomic sequences for putative RNA genes have been devised in the
last few years.
Structure-based searches use the known secondary structure of the major
classes of functional RNAs. Programs such as
RNAmot
(34),
tRNAscan
(83),
HyPa
(163),
RNAMotif
(88),
bruce
(76), and many others exploit this ave-
nue. An interesting variant that makes use of evolutionary computation is de-
scribed by (165). Nevertheless, all these approaches are restricted to searching
for new members of the few well-established families. The web-based resource
RNAGENiE
uses a neural network that has been trained on a wide variety of
functional RNAs (166). It is capable of detecting a wider variety of functional
RNAs.
