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Table 3 Recall rates of clustering of mRNA simulated reads (reads of length 200, k =2 and 2 clusters) for different measures, different types of errors and number of reads

From: Clustering of reads with alignment-free measures and quality values

Distance No errors Mismatch = 10% Insertion = 10% Deletion = 10%
    Mismatch = 10% Mismatch = 10%
500 reads
\(D^{*}_{2}\) 0.86445887 0.83981814 0.79073482 0.80640363
\(D^{*q}_{2}\) AQP 0.86441326 0.86694192 0.86376933 0.85925575
\(D^{*q}_{2}\) AQP q-red 0.86441326 0.86375045 0.85782736 0.85818320
\(D^{*q}_{2}\) AWP 0.86723257 0.85428665 0.84756397 0.85088665
\(D^{*q}_{2}\) AWP q-red 0.86723257 0.85613671 0.85305013 0.85504185
L 2 0.86114263 0.85504302 0.85105192 0.85118905
D 2 0.86258900 0.85247832 0.84995366 0.85110380
KL 0.87235487 0.85916040 0.85026923 0.85475077
Simm, KL 0.86712365 0.85695963 0.84730941 0.85418699
1000 reads
  0.86594479 0.83906192 0.78782226 0.80686962
\(D^{*q}_{2}\) AQP 0.86599548 0.86400152 0.86423642 0.85659489
\(D^{*q}_{2}\) AQP q-red 0.86600096 0.86099042 0.85469494 0.85441545
\(D^{*q}_{2}\) AWP 0.86790093 0.85433807 0.84230775 0.84839892
\(D^{*q}_{2}\) AWP q-red 0.86790093 0.85770704 0.85062824 0.85104321
L 2 0.86216987 0.85477261 0.84904670 0.85024936
D 2 0.86058645 0.85312555 0.84767965 0.85043005
KL 0.87048717 0.85667036 0.85002398 0.85088847
Simm, KL 0.86919513 0.85488101 0.84896184 0.84950072
2000 reads
\(D^{*}_{2}\) 0.86307749 0.83460148 0.78680210 0.81273009
\(D^{*q}_{2}\) AQP 0.86306541 0.86490821 0.86432381 0.85783381
\(D^{*q}_{2}\) AQP q-red 0.86306541 0.86129411 0.85330127 0.85111236
\(D^{*q}_{2}\) AWP 0.86305839 0.85432677 0.84295441 0.85043303
\(D^{*q}_{2}\) AWP q-red 0.86306276 0.85799349 0.84868427 0.85289041
L 2 0.86125521 0.85265296 0.84487856 0.84694314
D 2 0.85971734 0.85283644 0.84325115 0.84899721
KL 0.86990625 0.85621086 0.84559916 0.85108524
Simm, KL 0.86827273 0.85433859 0.84321338 0.85010800
3000 reads
\(D^{*}_{2}\) 0.86131992 0.83027426 0.79355066 0.81057286
\(D^{*q}_{2}\) AQP 0.86134064 0.86519721 0.86235323 0.85792626
\(D^{*q}_{2}\) AQP q-red 0.86128705 0.85978356 0.85252267 0.85262847
\(D^{*q}_{2}\) AWP 0.86477422 0.85334750 0.84374378 0.84947286
\(D^{*q}_{2}\) AWP q-red 0.86477422 0.85637033 0.84850933 0.85162186
L 2 0.86370337 0.85297951 0.84525794 0.84901375
D 2 0.86242736 0.85271505 0.84384526 0.84832590
KL 0.86934393 0.85488377 0.84531374 0.85014251
Simm, KL 0.86580244 0.85353783 0.84308462 0.84878825
\(D^{*}_{2}\) 0.86179886 0.83217374 0.79345107 0.80917623
\(D^{*q}_{2}\) AQP 0.86166330 0.86412834 0.86385592 0.86064860
\(D^{*q}_{2}\) AQP q-red 0.86166519 0.85559541 0.85133437 0.85345570
\(D^{*q}_{2}\) AWP 0.86317541 0.85224352 0.84168072 0.84837070
\(D^{*q}_{2}\) AWP q-red 0.86317541 0.85543020 0.84770910 0.85121979
L 2 0.86262435 0.85243814 0.84436053 0.84898583
D 2 0.86122271 0.85167640 0.84308556 0.84801094
KL 0.86792997 0.85473650 0.84431637 0.84985690
Simm, KL 0.86488656 0.85297623 0.84262083 0.84815285
  1. Best results are in bold.