# Perl-RDB # # PROGRAM AQUA # DATE file generated on Wed May 1 0:24:53 CET 1996 # # OVERALL SCORES: # nPairs 4 # nPred 4 # nTrue 2 # rankFst 1 # rankAcc 50 # rankCov 100 # rankFaTb 2 # zHisto 3 , 2 # zNocc 4 , 4 # zNcor 2 , 2 # zAcc 50 , 50 # zCov 100 , 100 # # NOTATION OVERALL SCORES: # nPairs number of pairs in predicted alignment # nPred number of predicted pairs included in analysis # (i.e. not found in Exclude set, zscore, and length ok asf.) # nTrue number of pairs in true alignment that were not excluded # (i.e. found in Search set NOT found in Exclude set, zscore ok asf.) # rankFst rank of first correct hit # rankAcc 100 * (number of correct hits/number of hits) # note: appropriately changed if Exclude and Search set given! # rankCov 100 * (number of correct hits/number of true hits) # note: appropriately changed if Exclude and Search set given! # rank50 rank at which number of correct hits equals number of false hits # rankFaTb rank at which number of false positive hits above this rank (fA) # equals the number of correct hits below this rank (tB) # zHisto intervals for z-dependent rank analysis # (take all pairs i with z(i) > zHisto) # zNocc number of pairs with z(i) > zHisto # zNcor number of correctly predicted pairs with z(i) > zHisto # zAcc z-dependent accuracy = 100 * (zNcor/zNocc) # zCov z-dependent coverage = 100 * (zNcor/[min(nTrue,zNocc)]) # shiftAcc AQUAshift accuracy (see below) for first correct hit # shiftCov AQUAshift coverage (see below) for first correct hit # shiftPide AQUAshift percentage identity (see below) for first correct hit # # NOTATION RANK ANALYSIS: # *Pred describes the 'predicted' alignment # *True describes the 'true' alignment # # ok =1, hit was found in true alignment # incl =1, hit was NOT excluded, i.e.,found in 'to-be-excluded' list # (i) it was not found in 'to-be-excluded' list (e.g. as >25% seqide; # option: 'fileExclude=file') # (ii) rali=(2*lenAli)/(lenSeq+lenStr) was above the chosen cut-off # (option: 'inclRali=x') # (iii) the zscore was above the chosen cut-off (option 'inclRel=x') # whyExcl reason why excluded: # inExcl = found in Exclude set (given by user) # lenCut = 2*lenAli/(lenSeq+lenStr) < cut-off, provided # zCut = zscore (for Dali or prediction) < cut-off, provided # confCut= confidence < cut-off, provided # conf confidence for correctness of homologue(0=low, 9=high) # # rankPred rank in input file # rankAqua rank in analysis (skipping pairs that were excluded) # lenSeqPred length of 'Sequence', i.e. search protein # lenStrPred length of 'Structure', i.e. template protein from database # lenAliPred number of residues aligned in predicted pair # pidePred percentage of sequence identity (Nres identical/Nres aligned) # lenSeqTrue length of 'Sequence', i.e. search protein # (may differ from lenSeqPred, if e.g. only one chain, or domain) # lenStrTrue length of 'Structure', i.e. template protein # (may differ from lenSeqPred, if e.g. only one chain, or domain) # lenAliTrue number of residues aligned in true pair # pideTrue percentage of sequence identity (Nres identical/Nres aligned) # # zPred reliability (z-score, probability, energy) of the predicted pair # # NOTATION ALIGNMENT SHIFT ANALYSIS: # shiftAcc 100* (ShiftScore/lenAliTrue) # shiftPide 100* (number of residues correctly aligned/lenAliTrue), # i.e. the percentage of correctly aligned residues # shiftCov lenAliTrue/lenAliPred (note: if > 1 , this indicates # an overprediction) # shiftAccRan shiftAcc for a pair with the same N- and C-term as the # predicted alignment, but with randomly inserted gaps # (random background) # shift0 number of residues with a shift of 0 # shift1 number of residues with a shift of 1 # shift2 number of residues with a shift of 2 # shift3 number of residues with a shift of 3 # # NOTATION ALIGNMENT 3D ANALYSIS: # # # zDali significance of true alignment (DALI z-score) # rmsDali r.m.s.d. compiled by DALI # # NOTATION OVERALL AVERAGES: # the final rows contain the following information # note: columns that do not make sense are empty # ave averages over columns # var variance of averages # sum for shift histograms: sums over all occurrences of a shift of 0 - N # perc for shift histograms: percentages of all occurrences for shift of 0 - N # aveOk averages compiled only for correct hits # varOk variances thereof # #
| idSeq | idPred | idTrue | ok | incl | conf | whyExcl | rankPred | rankAqua | lenSeqPred | lenStrPred | lenSeqTrue | lenStrTrue | lenAliPred | lenAliTrue | pidePred | pideTrue | zPred | zscore1Pred | zDali | shiftAcc | shiftPide | shiftAccRan | shiftCov | shift0 | shift1 | shift2 | shift3 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1acf | 2btfP | 2btfP | 1 | 1 | 8 | 1 | 1 | 140 | 180 | 140 | 180 | 100 | 100 | 40 | 40 | 5.0 | 0.8 | 5.5 | 75 | 74 | 9 | 97 | 90 | 2 | 5 | 16 | |
| 1acf | 2btg | 0 | 1 | 0 | 2 | 2 | 140 | 160 | 0 | 0 | 90 | 0 | 30 | 0 | 3.0 | 0.7 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ||
| 1acf | 2btx | 0 | 1 | 0 | 3 | 3 | 140 | 200 | 0 | 0 | 120 | 0 | 50 | 0 | 4.0 | 0.6 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ||
| 1acf | 2btz | 2btz | 1 | 1 | 8 | 4 | 4 | 140 | 200 | 140 | 190 | 120 | 100 | 50 | 40 | 5.0 | 0.3 | 3.1 | 36 | 0 | 21 | 99 | 0 | 120 | 0 | 0 | |
| idSeq | idPred | idTrue | ok | incl | conf | whyExcl | rankPred | rankAqua | lenSeqPred | lenStrPred | lenSeqTrue | lenStrTrue | lenAliPred | lenAliTrue | pidePred | pideTrue | zPred | zscore1Pred | zDali | shiftAcc | shiftPide | shiftAccRan | shiftCov | shift0 | shift1 | shift2 | shift3 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ave | 140 | 185 | 140 | 185 | 107 | 100 | 42 | 40 | 4.2 | 0 | 2.1 | 55 | 37 | 15 | 98 | 45 | 61 | 2 | 8 | ||||||||
| sum | 90 | 122 | 5 | 16 | |||||||||||||||||||||||
| perc | 38 | 52 | 2 | 6 | |||||||||||||||||||||||
| aveOk | 140 | 190 | 110 | 45 | 5.0 |