Exploiting single-molecule transcript sequencing for eukaryotic gene prediction

Table 4 Parameter training and results on ab initio performance

Training settings		Parameter evaluation on 542 test genes
Training genes	Setting	Exon level		Transcript level		Sum	Rank	UTR bases
		Sensitivity	Precision	Sensitivity	Precision			Sensitivity	Precision
288	Manual only	0.759	0.486	0.356	0.201	1.802	9	0.484	0.359
800	-	0.800	0.509	0.424	0.233	1.966	7	0.509	0.350
1,200	-	0.808	0.511	0.445	0.244	2.008	3	0.502	0.358
1,200	New species	0.812	0.491	0.380	0.213	1.900	8	0.480	0.357
1,200	SMRT only	0.820	0.517	0.448	0.245	2.030	2	0.515	0.374
1,200	No UTR	0.808	0.511	0.445	0.244	2.008	3	0.502	0.358
1,200	3 opt. rounds	0.808	0.511	0.445	0.244	2.008	3	0.502	0.358
1,200	6 opt. rounds	0.808	0.511	0.445	0.244	2.008	3	0.502	0.358
2,000	-	0.830	0.515	0.458	0.248	2.051	1	0.508	0.363
A. thaliana parameters	-	0.810	0.391	0.384	0.151	1.736	10	0.623	0.287

Manual only: refers to 400 manually curated genes of which 288 were used for training and the remainder as test set. A. thaliana parameters: refers to the default A. thaliana parameters as provided by Stanke et al. Rank: calculated from the sum of the sensitivity and the precision for exons, transcripts, and UTR bases. New species: refers to calculating B. vulgaris parameters from scratch using ‘new_species.pl’ (part of the AUGUSTUS pipeline). Opt. round: refers to the number of optimization rounds when running optimize_augustus.pl; the default was nine rounds. SMRT only: refers to training including only SMRT-validated genes. No UTR: refers to not setting the ‘--UTR = on’ parameter when using optimize_augustus.pl

ISSN: 1474-760X