KnotAli: informed energy minimization through the use of evolutionary information

BMC Bioinformatics

Table 5 Comparison of KnotAli with RNAalifold, Hxmatch, and Cacofold

Family	KnotAli			RNAalifold			Hxmatch			Cacofold
Family	Sen	ppv	F	Sen	ppv	F	Sen	ppv	F	Sen	ppv	F
(a) Input alignment created through MUSCLE
5s	.899	.876	.887	.761	.884	.817	.424	.917	.579	.835	.859	.846
16s	.494	.501	.494	.506	.748	.602	.385	.724	.502	.172	.455	.250
23s	.589	.545	.566	.798	.767	.782	.552	.625	.587	.242	.341	.283
Group I intron	.490	.444	.461	.047	.588	.087	.034	.529	.064	.039	.300	.068
Group II intron	.177	.139	.154	0	0	0	.010	.108	.018	0	0	0
RNaseP	.498	.491	.493	.235	.602	.334	.135	.699	.225	.164	.552	.251
SRP	.580	.556	.564	.165	.764	.241	.166	.897	.25	.186	.496	.255
Telomerase	.289	.233	.256	.508	.636	.563	.292	.711	.413	.380	.480	.423
tmRNA	.491	.468	.477	.255	.803	.386	.176	.852	.291	.234	.868	.367
tRNA	.950	.917	.932	.931	.972	.949	.764	.974	.854	.886	.970	.925
(b) Input alignment created through MAFFT
5s	.902	.871	.885	.644	.843	.729	.385	.927	.541	.739	.852	.790
16s	.548	.495	.519	.548	.794	.647	.440	.802	.567	.198	.467	.277
23s	.329	.468	.361	.795	.771	.783	.563	.627	.593	.281	.336	.281
Group I intron	.424	.378	.396	.036	.719	.068	.036	.719	.069	.051	.384	.090
Group II intron	.382	.244	.295	.106	.773	.186	.103	.580	.175	.105	.920	.187
RNaseP	.592	.583	.585	.207	.759	.322	.067	.700	.122	.301	.639	.400
SRP	.420	.416	.415	.078	.661	.129	.078	.885	.134	.148	.377	.206
Telomerase	.243	.186	.211	.25	.361	.294	.255	.483	.333	.442	.517	.475
tmRNA	.504	.492	.495	.196	.799	.313	.047	.435	.084	.255	.650	.362
tRNA	.898	.878	.886	.8	.931	.855	.642	.940	.758	.853	.925	.882*

Each column corresponds to algorithm used and each sub-column represents a metric: F-measure, Sensitivity or PPV. BOLD represents the significantly highest accuracy compared to others. In the case of two algorithms whose accuracy outperformed the rest while not significantly better than each other, both were represented in bold. An accompanying * is then used to denote a p-value close to but not below .05.

ISSN: 1471-2105