Table 1.

Representative software and resources used in expertcuration

Curation step	Software/database	Purpose	Weblink	Ref.
Sequence curation
Identify homologs	BLAST	Sequence alignment	https://blast.ncbi.nlm.nih.gov/	[83]
Document inconsistencies	Ensembl	Phylogenetic resources	https://www.ensembl.org/	[84]
	T-Coffee	Sequence difference (e.g., alternative splicing) analysis	https://www.ebi.ac.uk/Tools/msa/tcoffee/	[85]
	MUSCLE		https://www.ebi.ac.uk/Tools/msa/muscle/	[86]
	ClustalW		https://www.ebi.ac.uk/Tools/msa/clustalw2/	[87]
Sequence analysis
Predict topology	SignalP	Signal peptide prediction	http://www.cbs.dtu.dk/services/SignalP/	[88]
	TMHMM	Transmembrane domain prediction	http://www.cbs.dtu.dk/services/TMHMM/	[89]
Predict PTMs	NetNGlyc	N-glycosylation site prediction	http://www.cbs.dtu.dk/services/NetNGlyc/	[90]
	Sulfinator	Tyrosine sulfation site prediction	https://web.expasy.org/sulfinator/	[91]
Identify domains	InterPro	Retrieval of motif matches	https://www.ebi.ac.uk/interpro/	[92]
	REPEAT (REP tool)	Identification of repeats	https://www.ebi.ac.uk/interpro/	[93]
Literature curation
Identify relevant literature	PubMed	Literature resources	https://pubmed.ncbi.nlm.nih.gov/	[94]
	iHOP		https://bio.tools/ihop	[95]
Extract named entities	PubAnnotation	Information extraction	http://pubannotation.org/	[96]
	PubTator		https://www.ncbi.nlm.nih.gov/research/pubtator/	[97]
Assign GOs	GO	Gene ontology terms	http://geneontology.org/	[14]
Family curation	BLAST	Sequence alignment	https://blast.ncbi.nlm.nih.gov/	[83]
Evidence attribution	ECO	Evidence code ontology	http://www.evidenceontology.org/	[98]

Note: A complete set of the software, including the detailed versions of the software, can be found in UniProt manual curation standard operating procedure documentation (www.uniprot.org/docs/sop_manual_curation.pdf). PTM, post-translational modification.