Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species

Table 2 Percentage of residues left unmatched.

		BLAT	Exnrt.	BLAT	Exnrt.
Species	Scipio (automatic assembling)	with manual assembling		without assembling
Bombyx mori p50T	15.03	15.41	17.03	43.61	43.64
Drosophila simulans	7.11	7.44	8.14	31.83	30.33
Bombyx mori str. Dazao	7.93	8.43	7.86	36.09	36.38
Nasonia vitripennis (contigs)	0.20	0.60	0.45	10.17	9.38
Nasonia vitripennis (scaffolds)	1.11	1.50	1.38	3.70	3.89
Drosophila sechellia	0.11	0.45	0.95	9.05	10.14
Aedes aegypti	0.73	1.01	0.21	10.43	10.22
Daphnia pulex	1.26	1.84	1.33	1.84	1.88
Anopheles gambiae	0.02	0.31	0.26	0.31	0.63
Drosophila melanogaster	0.00	0.32	0.05	0.32	0.05
Aspergillus niger	0.01	0.18	0.08	0.18	2.63
Homo sapiens	0.06	0.92	0.10	0.92	0.10
Macaca mulatta	2.29	3.09	2.31	3.09	7.82
total	1.67	2.16	1.87	8.24	8.71

The percentage of residues of the query sequences that the compared tools failed to recover from the target sequence. To gain comparable results, the hits proposed by BLAT and Exonerate were assembled together manually: a collection of best-scoring non-overlapping hits was chosen for each query. The last two columns show the results if only the best-scoring hit for each query was used.

ISSN: 1471-2105