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Abstract:
The functions of non-coding RNAs
are strongly related to their secondary structures,
but it is known
that a secondary structure prediction of a single sequence is not reliable.
Therefore, we have to collect similar RNA sequences
with a common secondary structure
for the analyses of a new non-coding RNA
without knowing the exact secondary structure itself.
Therefore, the sequence comparison in searching similar RNAs should consider
not only their sequence similarities but their potential secondary structures.
Sankoffamp;lsquo;s algorithm predicts the common secondary structures of the sequences,
but it is computationally too expensive to apply to large-scale analyses.
Because we often want to compare a large number of cDNA sequences
or to search similar RNAs in the whole genome sequences,
much faster algorithms are required.
We propose a new method of comparing RNA sequences
based on the structural alignments
of the fixed-length fragments of the stem candidates.
The implemented software,
SCARNA (Stem Candidate Aligner for RNAs),
is fast enough to apply to the long sequences
in the large-scale analyses.
The accuracy of the alignments is better or comparable
to the much slower existing algorithms.
