Results based on alternative datasets (database alignments as well)

datasets taken from ILM
[ Ruan et al., 2003 ]

The hxmatch 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.

    ilm hxmatch -A
Raw   Filled
Nseq eta SS SP PK SS SP compared PK SS SP compared
5S rRNA 12 0.61 83 100 0/0 65 100 i5src.ps 0/0 83 89 i5sfc.ps
SRP RNA 12 0.50 96 79 1/1 93 94 isrprc.ps 1/1 96 81 isrpfc.ps
tmRNA 8 0.60 90 71 4/4 84 91 itmrc.ps 4/4 95 92 itmfc.ps
Telomerase RNA 9 0.59 80 53 1/1 42 84 itelorc.ps 1/1 54 42 itelofc.ps
16S rRNA 10 0.72 74 66 1/2 72 80 i16src.ps 1/2 81 76 i16sfc.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 ).
Nseq gives the number of sequences contained in the alignment;
eta is the mean pairwise sequence identity of the alignment.
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;
Compared gives the predicted structure compared to the reference structure in linked diagram representation.
Base pairs drawn in black are present in both the predicted structure and the reference structure (true positives). Red base pairs are only present in our prediction, but not in the reference (false positives). And base pairs which are not contained in the prediction, but are part of the reference structure (false negatives) are drawn in green.

The slight difference of SS and SP of ilm compared to the values given in Ruan et al., 2003 is due to the use of a later version of ilm.

Last modified: 2004-09-02 16:53:34 xtina