Table 3.

Prediction algorithm performance comparison and statistics

Strain ID	Gene predictions by GeneMark	Gene predictions by Glimmer3	Gene predictions by BLAST	ORFs with full consensusa	ORFs with partial consensusb	Total gene predic- tions reportedc	tRNAs predicted by tRNAScan-SE
NM13220	2530	2725	1353	1325	974	2299	52
NM10699	2366	2494	1317	1284	826	2110	51
NM15141	2411	2578	1369	1343	841	2184	57
NM9261	2370	2553	1341	1308	802	2110	51
NM18575	2751	2927	1495	1448	1023	2471	63
NM5178	2377	2510	1315	1281	816	2097	52
NM15293	2062	2040	1285	1261	802	2063	51
BBE001	4793	4793	2744	2732	2067	4799	48
BBF579	4649	4646	2652	2635	2021	4656	48

Data for each strain are presented in rows. Prediction counts from the three standalone gene prediction methods are presented. Counts of protein-coding gene predictions reported by our algorithm and tRNA genes are also shown. Data presented are based on the automatic combined assemblies from Table 2.

^aNumber of ORFs with protein-coding gene predictions where all three predictors agreed exactly or with a slight difference in the predicted start site.

^bORFs where only two of the three predictors made a prediction.

^cTotal protein-coding gene predictions reported by the pipeline.