Automatically extracting functionally equivalent proteins from SwissProt

BMC Bioinformatics

Table 5 Comparing FOSTA with Inparanoid

Code	Species	Pairs	Matches	Mismatches	% match	Overlooked	Rejected
APIME	Apis mellifera	1	1	0	100.00%	-	-
BOSTA	Bos taurus	3508	3451	57	98.38%	1	56
CANFA	Canis familiaris	533	520	13	97.56%	1	12
CIOIN	Ciona intestinalis	6	5	1	83.33%	0	1
DANRE	Danio rerio	1246	1192	54	95.67%	21	33
DICDI	Dictyostelium discoideum	85	69	16	81.18%	0	16
DROME	Drosophila melanogaster	878	712	166	81.09%	14	152
DROPS	Drosophila pseudoobscura	73	67	6	91.78%	0	6
GALGA	Gallus gallus	1360	1297	63	95.37%	12	51
GASAC	Gasterosteus aculeatus	1	1	0	100.00%	-	-
MACMU	Macaca mulatta	214	207	7	96.73%	0	7
MONDO	Monodelphis domestica	22	21	1	95.45%	0	1
MUSMU	Mus musculus	12063	11960	103	99.15%	18	85
ORYSA	Oryza sativa	1	0	1	0.00%	0	1
PANTR	Pan troglodytes	412	408	4	99.03%	1	3
RATNO	Rattus norvegicus	5076	5005	71	98.60%	6	65
SACCE	Saccharomyces cerevisiae	1213	787	426	64.88%	49	377
TETNI	Tetraodon nigroviridis	6	6	0	100.00%	-	-
XENTR	Xenopus tropicalis	371	364	7	98.11%	2	5
-	All species	27069	26073	996	96.32%	125	871

Code: The species code as used by Inparanoid; Species: The full species name; Pairs: The number of one-to-one orthologue pairs described by Inparanoid between Species and Human; Matches: The number of one-to-one Inparanoid orthologue pairs (IPs) that are also found by FOSTA; Mismatches: The number of IPs pairs that are not found by FOSTA; % match: The percentage of IPs that are also found by FOSTA; Overlooked: The number of IPs where FOSTA assigns a different protein from the Species to the FOSTA family of the human protei; Rejected: The number of IPs where FOSTA does not assign any protein from the Species to the FOSTA family of the human protein.

ISSN: 1471-2105