2003
DOI: 10.1016/s1476-9271(02)00094-4
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Automated annotation of microbial proteomes in SWISS-PROT

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Cited by 129 publications
(90 citation statements)
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“…The curated part of Swiss-Prot database was selected because of the extent and quality of annotations associated with each protein sequence [25], and the PDB provides an archive of experimentally-determined three-dimensional protein structures. BLAST matches were examined sequentially, searching for a match with direct experimental verification of the function.…”
Section: Manual Annotation Evidence Rating System and Comparison Genmentioning
confidence: 99%
See 1 more Smart Citation
“…The curated part of Swiss-Prot database was selected because of the extent and quality of annotations associated with each protein sequence [25], and the PDB provides an archive of experimentally-determined three-dimensional protein structures. BLAST matches were examined sequentially, searching for a match with direct experimental verification of the function.…”
Section: Manual Annotation Evidence Rating System and Comparison Genmentioning
confidence: 99%
“…The protein sequence for each gene was searched against the Swiss-Prot and Protein Data Bank (PDB) databases using BLAST [24] to identify the most closely related, experimentally characterized homolog available in the literature. The curated part of Swiss-Prot database was selected because of the extent and quality of annotations associated with each protein sequence [25], and the PDB provides an archive of experimentally-determined three-dimensional protein structures. BLAST matches were examined sequentially, searching for a match with direct experimental verification of the function.…”
Section: Supplementary Informationmentioning
confidence: 99%
“…For the lifestyle analysis, we have manually grouped species into two groups: parasitic and non-parasitic (following the HAMAP database (Gattiker et al, 2003) and (Fitz-Gibbon and House, 1999;House and Fitz-Gibbon, 2002)). We classify as parasitic all organisms that are listed as symbionts, endosysmbionts, or parasites, because organisms living in any of these ecological relationships have been found to have suffered a genome reduction over time (Andersson and Kurland, 1998).…”
Section: Analysis Of Group Patterns In Protein Family Size Distributionsmentioning
confidence: 99%
“…The use of a whole protein classification database, such as PIRSF, combined with an insistence that predicted members of a given family exhibit (near) end-to-end similarity, obviates such problems. Other predominantly whole protein classification databases (which may or may not also contain domain families) include COGs, TIGRFAMs (Haft et al, 2003), PANTHER (Mi et al, 2005), and HAMAP (Gattiker et al, 2003).…”
Section: Hierarchical Whole-protein Classificationmentioning
confidence: 99%
“…PIR has developed manually-curated Site Rules (PIRSRs) and Name Rules (PIRNRs), each of which (described in detail below) is based on curated protein families of the PIRSF system. SIB has developed curated rules based on the curated HAMAP family system (Gattiker et al, 2003). EBI has multiple systems-the manually curated RuleBase system (Biswas et al, 2002) and the automatically generated Spearmint (Kretschmann et al, 2001) and Xanthippe (Wieser et al, 2004) rules.…”
Section: Rule-based Automated Annotationmentioning
confidence: 99%