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.

  hxmatch -A
PK Raw Filled
SS SP prediction result compared SS SP prediction result compared
SRP RNA 1/1 91.9 84.9 srpr.db srpr.list srprc.ps 96.5 82.2 srpf.db srpf.list srpfc.ps
tmRNA 4/4 84.0 90.8 tmr.db tmr.list tmrc.ps 95.3 91.8 tmf.db tmf.list tmfc.ps
RNase P RNA 2/2 77.4 88.9 rnaser.db rnaser.list rnaserc.ps 92.7 89.1 rnasef.db rnasef.list rnasefc.ps
Telomerase RNA 1/1 86.3 79.3 telor.db telor.list telorc.ps 86.3 59.1 telof.db telof.list telofc.ps
16S rRNA 1/2 77.6 85.7 16sr.db 16sr.list 16src.ps 85.1 80.4 16sf.db 16sf.list 16sfc.ps

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