Results based on the database alignments
All predictions were calculated using hxmatch -A with default
parameters. The "-A" option means, that the RNAalifold (see
also Vienna RNA package,
v1.5beta version)
prediction is included in the computation of the initial weight matrix.
Raw corresponds to the consensus structures as predicted by
hxmatch -A, filled are the
structures obtained by computing the thermodynamically most favorable
structure consistent with the consensus structure (using
RNAfold
-C ).
PK =
(number of correctly predicted pseudoknots)/(number of pseudoknots in the
reference structure);
SS = 100*TP/RP and SP = 100*TP/(TP+FP);
RP = number of
base pairs in
the reference structure;
TP = number of true positive
predicted base
pairs;
FP = number of false positive predicted base pairs;
The prediction results are given in two different file
formats: "*.db"
contains the predicted structure of the reference organism in
dot-bracket format, "*.list" lists the predicted base pairs ('U'
corresponds to base pairs drawn in the upper half plane of the linked
diagram representation, 'L' corresponds to base pairs drawn in the
lower half plane of the linked
diagram representation).
For details of the alignments used, see Data.
Last modified: 2004-09-02 17:14:25 xtina