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RNALfold - calculate locally stable secondary structures of RNAs
RNALfold [-L span] [-T temp] [-4] [-noLP]
[-noGU] [-noCloseGU] [-e 1|2]
[-P paramfile] [-nsp pairs]
RNALfold computes locally stable RNA secondary structure
with a maximal base pair span. For a sequence of length n and a
base pair span of L the algorithm uses only O(n+L*L) memory and
O(n*L*L) CPU time. Thus it is practical to "scan" very large
genomes for short RNA structures.
Output consists of a list of secondary structure components of
size <= L, one entry per line. Each output line contains the
predicted local structure its energy in kcal/mol and the starting
position of the local structure.
- -L span
- Set the maximum allowed separation of a base pair to span. I.e.
no pairs (i,j) with j-i>span will be allowed.
The -T, -d -4, -noGU,
-noCloseGU, -e, -P, -nsp, options work
as in RNAfold. Most tests were done using "-d2 -noLP", other
dangling end settings may still be buggy.
I.L. Hofacker, B. Priwitzer, and P.F. Stadler "Prediction of
Locally Stable RNA Secondary Structures for Genome-Wide Surveys"
Bioinformatics, 20, 186-190 (2004)
This man page documents version 1.8.5 Vienna RNA Package.
Ivo L Hofacker, Peter F Stadler.
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Time: 07:19:16 GMT, February 23, 2011