Clustering of reads with alignment-free measures and quality values

Comin, Matteo; Leoni, Andrea; Schimd, Michele

doi:10.1186/s13015-014-0029-x

Algorithms for Molecular Biology

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

Best results are in bold.

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