The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

By Brigitte Boeckmann, Amos Bairoch, Rolf Apweiler, M. Blatter, A. Estreicher, Elisabeth Gasteiger, Maria Jesus Martin, Karine Michoud, C. O’Donovan, I. Phan and 2 more. 2003

3,873 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

Citations in the corpus

ProGen: Language Modeling for Protein Generation (2020, methodology): “We utilize all protein sequences and associated tags available in Uniparc (Leinonen et al., 2004), Unipro-tKB (Bairoch et al., 2005), SWISS-PROT (Bairoch et al., 2004), TrEMBL (Boeckmann et al., 2003), Pfam (Bate-man et al., 2004), and NCBI taxonomic information (Feder-hen, 2012).”
The Universal Protein Resource (UniProt) (2004, background): “Previously, Swiss-Prot + TrEMBL ( 1 ) and PIR-PSD (2) coexisted as protein databases with differing sequence coverage and annotation priorities.”
UniProt archive (2004, methodology): “New and updated protein sequences are loaded daily from public databases including SWISS-PROT, TrEMBL, PIR-PSD, EMBL (Stoesser et al., 2003), Ensembl (Hubbard et al., 2002), PDB (Westbrook et al., 2003), IPI (http://www.ebi.ac.uk/IPI), RefSeq (Pruitt and Maglott, 2001), FlyBase (The FlyBase Consorti”
Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. (2005, methodology): “Sequence conservation and surface accessibility For each of the 86 proteins in our data set, close protein homologs were identified by searching SWISS-PROT (Boeckmann et al., 2003) for mammalian proteins with entry names with identical prefix.”
Impact of selection, mutation rate and genetic drift on human genetic variation. (2003, methodology): “Protein sequences for human and mouse genes were obtained by extracting all entries from the SWALL database (35) annotated as “Homo sapiens” and “Mus musculus” in the organism field.”
PreBIND and Textomy – mining the biomedical literature for protein-protein interactions using a support vector machine (2003, methodology): “The dictionary of protein names was derived from the 'short description of entries' field in SwissProt [23].”
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics (2003, background): “38 (Boeckmann et al. 2003); or (2) if it did not have any BLASTP hit in Caenorhabditis or SwissProt of E-value ,10 10 with the SEG filter on (Wootton and Federhen 1996) or Evalue ,10 20 with SEG off; or (3) if it had a within-species sequence match, but no cross-species sequence match and was less t”
Choosing BLAST options for better detection of orthologs as reciprocal best hits (2008, background): “uk/GenomeReviews/), the HAMAP project (Boeckmann et al., 2003; Gattiker et al., 2003), or even those re-annotations produced by particular research groups (e.”
OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements (2005, positive): “The consistency verification is extensive, and includes comparison between DNA and amino acid sequence, check for presence of start and stop codon, removal of fragments shorter than 50 amino acids, removal of duplicated sequences (sequences with >99% identity), verification of the total number of en”
MultiSeq: unifying sequence and structure data for evolutionary analysis (2006, background): “The total size of the sequence databases (NCBI [7,8], EMBL [9], DDBJ [10], JGI [11], RDP [12], Swiss-Prot/TrEMBL [13], CRW [14], Bayreuth tRNA compila-tions [15], and the Genomic tRNA Database [16]) is several orders of magnitude greater than that of the structure databases.”
Human protein reference database—2006 update (2005, background): “HPRD can be queried through gene symbols or a variety of database accession numbers such as RefSeq (10), OMIM (11), Swiss-Prot (12), HPRD and Entrez Gene (13).”
The HSP70 heat shock response in the Antarctic fish Harpagifer antarcticus (2007, positive): “Consensus sequences were database searched using WU-blast2 (WU-blastx) (Altschul et al, 1997) against Uniprot (Boeckmann et al, 2003; Wu et al, 2006) to assign their HSP identity.”
A new disease-specific machine learning approach for the prediction of cancer-causing missense variants (2011, methodology): “Neutral variants are from Swiss-Prot database [47] or generated by CHASM.”
The PredictProtein server (2003, methodology): “CHOP (33) is a hierarchical procedure that chops proteins into structural domain-like fragments through similarity to domains of known structure [taken from PrISM (34)], or to Pfam-A domain-like fragments (35) [searches through HMMer (36)], or to full-length natively expressed proteins taken from Sw”