Identification and correction of abnormal, incomplete and mispredicted proteins in public databases

Nagy, Alinda; Hegyi, Hédi; Farkas, Krisztina; Tordai, Hedvig; Kozma, Evelin; Bányai, László; Patthy, László

doi:10.1186/1471-2105-9-353

BMC Bioinformatics

Table 2 MisPred analysis of TrEMBL entries

From: Identification and correction of abnormal, incomplete and mispredicted proteins in public databases

UniProtKB/TrEMBL
Conflict 1	Number of proteins	Identified as containing an extracellular domain	Percentage	Identified as suspicious by MisPred	Percentage*	False positives	Percentage*	True errors	Percentage*	Annotated as fragment or chimera by UniProt	Identified as abnormal only by MisPred
Homo sapiens	52237	6732	12.9%	3907	58.0%	ND	ND	ND	ND	ND	ND
Conflict 2	Number of proteins	Identified as containing an extra- and an intracellular domain	Percentage	Identified as suspicious by MisPred	Percentage*	False positives	Percentage*	True errors	Percentage*	Annotated as fragment or chimera by UniProt	Identified as abnormal only by MisPred
Homo sapiens	52237	58	0.11%	9	15.5%	9	15.5%	0	0.0%	0	0
Conflict 3	Number of proteins			Identified as suspicious by MisPred	Percentage*	False positives	Percentage*	True errors	Percentage*	Annotated as fragment or chimera by UniProt	Identified as abnormal only by MisPred
Homo sapiens	52237			0	0.0%	0	0.0%	0	0.0%	0	0
Conflict 4	Number of proteins	Proteins containing domains suitable for the study of domain integrity	Percentage	Identified as suspicious by MisPred	Percentage*	False positives	Percentage*	True errors	Percentage*	Annotated as fragment or chimera by UniProt	Identified as abnormal only by MisPred
Homo sapiens	52237	17073	32.7%	2531	14.8%	ND	ND	ND	ND	ND	ND
Conflict 5	Number of proteins			Identified as suspicious by MisPred	Percentage*	False positives	Percentage*	True errors	Percentage*	Annotated as fragment or chimera by UniProt	Identified as abnormal only by MisPred
Homo sapiens	52237			172	0.33%	0	0.00%	172	0.33%	85	87
Mus musculus	50304			40	0.08%	ND	ND	ND	ND	ND	ND
Rattus norvegicus	8557			5	0.06%	ND	ND	ND	ND	ND	ND
Gallus gallus	5549			6	0.11%	ND	ND	ND	ND	ND	ND
Danio rerio	19623			387	1.97%	ND	ND	ND	ND	ND	ND
Caenorhabditis elegans	30000			0	0.00%	0	0	0	0	0	0
Drosophila melanogaster	26947			49	0.18%	ND	ND	ND	ND	ND	ND

*Values for suspicious, false positive and true positive sequences are expressed as percentage of the proteins relevant for the given conflict.
ND – not determined

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ISSN: 1471-2105

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