ライフサイエンスコーパス: SWISS-PROT

1 in the EMBL Nucleotide Sequence Database and SWISS-PROT.

2 in the EMBL Nucleotide Sequence Database and SWISS-PROT.

3 diction using the language and the syntax of SWISS-PROT.

4 ow includes proteins from both SP-TrEMBL and SWISS-PROT.

5 structures covering 33% of all sequences in SWISS-PROT.

6 structures covering 36% of all sequences in Swiss-Prot.

7 in the EMBL Nucleotide Sequence Database and SWISS-PROT.

8 gy (GO) annotation of a sub-set of UniProtKB/Swiss-Prot.

9 n databases, which only include sequences in Swiss-Prot.

10 ch would facilitate text-mining of UniProtKB/Swiss-Prot.

11 487 CVD-related proteins was extracted from SWISS-PROT.

12 in the EMBL Nucleotide Sequence Database and SWISS-PROT.

13 ation for fewer than half of all proteins in SWISS-PROT.

14 ly diverse categories of human proteins from SWISS-PROT.

15 in the EMBL Nucleotide Sequence Database and SWISS-PROT.

16 in knowledge about the Keyword annotation in SWISS-PROT.

17 Over 54% of proteins in SWISS-PROT-35 and SP-TrEMBL-5 match a Pfam family.

18 These Pfam families match 63% of proteins in SWISS-PROT 37 and TrEMBL 9.

19 071 families, which match 69% of proteins in SWISS-PROT 39 and TrEMBL 14.

20 trinsic disorder in eukaryotic proteins from SWISS-PROT (47 +/- 4%) and in nonhomologous protein segm

21 drial and extracellular animal proteins from Swiss-Prot 50.2.

22 ified enzyme as the open reading frame yjjT (SWISS-PROT accession number ).

23 is contained in databanks such as UniProtKB/Swiss-Prot and a manual analysis of these data allow FEP

24 tSubP on two independent data sets, one from Swiss-Prot and another containing green fluorescent prot

25 ding SGD, YPD and WormPD, Unigene, dbEST and SWISS-PROT and can be accessed at http://genome-www.stan

26 antify 11,352 gene products that span 70% of Swiss-Prot and capture protein regulation across the ful

27 s a source of re-annotated sequences for the SWISS-PROT and Colibri databases.

28 243 organisms available in public databases (SWISS-PROT and EMBL).

29 ases are extensively cross-referenced to the SWISS-PROT and GenBank databases.

30 The search engine allows one to search over SWISS-PROT and GenBank fields and then follow the links

31 nstructed using information contained in the SWISS-PROT and GenBank sequence databases.

32 ately 300,000 protein sequences sampled from Swiss-Prot and GenBank.

33 Two new compact databases are created from Swiss-Prot and GOA databases.

34 ,747 proteins for which the manually curated Swiss-Prot and KEGG databases have agreeing Enzyme Commi

35 blic databases including UniGene, LocusLink, SWISS-PROT and OMIM.

36 rotein sequence data compilations, including SWISS-PROT and the Entrez system of the NCBI.

37 protein sequence data compilations including SWISS-PROT and theEntrezsystem of the NCBI.

38 InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1,000,000 hits from 462

39 InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1000000 hits from 26433

40 fy the redundancy present within and between SWISS-PROT and TrEMBL and its subsequent removal.

41 ry database ensured the comprehensiveness of SWISS-PROT and TrEMBL but introduced some degree of redu

42 erPro covers over 78% of all proteins in the Swiss-Prot and TrEMBL components of UniProt.

43 results have been calculated for the entire Swiss-Prot and TrEmbl database sequences (approximately

44 etely sequenced genomes (currently 154), the Swiss-Prot and TrEMBL databases and other sequence colle

45 varsplic.pl uses information present in the SWISS-PROT and TrEMBL databases to create new records fo

46 earch against the Homo sapiens subset of the SWISS-PROT and TrEMBL databases, we identified 68 protei

47 well as all the eukaryotic sequences in the Swiss-Prot and TrEMBL databases.

48 All changed Swiss-Prot and TrEMBL entries are loaded into the UniSav

49 he UniProtKB, which contains only the latest Swiss-Prot and TrEMBL entry versions, the UniSave provid

50 tabase offers an automatic classification of SWISS-PROT and TrEMBL proteins into groups of related pr

51 The CluSTr (Clusters of SWISS-PROT and TrEMBL proteins) database offers an autom

52 NA sequences (EMBL-Bank), protein sequences (SWISS-PROT and TrEMBL), protein structure (MSD), whole g

53 m 264333 different proteins out of 384572 in SWISS-PROT and TrEMBL).

54 than 1,000,000 hits from 462,500 proteins in SWISS-PROT and TrEMBL).

55 erPro cover more than 74% of all proteins in SWISS-PROT and TrEMBL, an increase of nearly 15% since t

56 (3) Even if we combine SWISS-PROT and TrEMBL, some sequences from the full geno

57 rokaryotic genomes as well as sequences from SWISS-PROT and TrEMBL.

58 ranslated GenBank sequences and sequences in SWISS-PROT and TrEMBL.

59 ave) is a comprehensive archive of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entry versions.

60 nd standardizing the annotation in the MIPS, Swiss-Prot and YPD databases, and we achieve 75 % accura

61 rometry by searching E. coli proteins in the Swiss-Prot and/or NCBI databases.

62 elated to cell death from HUGO, Ensembl, and SWISS-PROT, and about 700 Drosophila genes from FlyBase

63 uman gene databases, e.g. GDB, LocusLink and SWISS-PROT, and approved gene symbols are carefully co-o

64 ists of about 830 000 non-redundant PIR-PSD, SWISS-PROT, and TrEMBL proteins organized with more than

65 SCOP, full-length sequence information from Swiss-Prot, and verified functional information from the

66 le to highlight inconsistencies in UniProtKB/Swiss-Prot annotation.

67 applied to text descriptions extracted from SWISS-PROT annotations.

68 The protein entries from SWISS-PROT are joined into clusters corresponding to alt

69 Using UniProtKB/Swiss-Prot as a case study, we address this concern via

70 re derived from the Protein Data Bank (PDB), Swiss-Prot, as well as Online Mendelian Inheritance in M

71 r the complete set of species represented in SWISS-PROT, as well as those stored at the NCBI.

72 (1) Contrary to claims by the SWISS-PROT authors, we conclude that SWISS-PROT does not

73 Biological knowledgebases, such as UniProtKB/Swiss-Prot, constitute an essential component of daily s

74 n bioinformatics databases such as UniProtKb/Swiss-Prot data entries and gene ontology concepts.

75 GENEBANK/EMBL/SWISS PROT database comparison of all sequences revealed

76 on the variant phenotypic annotation of the Swiss-Prot database and focused our analysis on nsSNPs h

77 structed a dataset of protein sequences from SWISS-PROT database and segmented them into 12 classes b

78 ch as a complete genome or the non-redundant SWISS-PROT database can be processed in a few hours on a

79 ly 6 min on a single core PC to scan a whole Swiss-Prot database of approximately 540 000 sequences a

80 nformation retrieved from the well annotated SWISS-PROT database together with sequence information f

81 TMLOOP was applied to the Swiss-Prot database, identifying 1392 confirmed membrane

82 ustive classification of all proteins in the SWISS-PROT database, into groups of related proteins.

83 Integrated with the latest version of the Swiss-Prot database, the data provide precise correlatio

84 y to the UPF 00096 family of proteins in the Swiss-Prot database.

85 re retrieved from both PIR-International and SWISS-PROT databases, including a large number of new me

86 otated for these cancer types in the OMIM or Swiss-Prot databases.

87 xible and robust parsing and editing of EMBL/SWISS-PROT databases.

88 es retrieved from both PIR-International and SWISS-PROT databases.

89 by the SWISS-PROT authors, we conclude that SWISS-PROT does not identify a significant number of exp

90 From there we map to Swiss-Prot entries and thence to the PDB.

91 tically creates protein reports from sets of SWISS-PROT entries, collating results into structured re

92 protein family reports from sets of related Swiss-Prot entries.

93 polypeptide chain of rabbit uterine smMLCK (Swiss-Prot entry P29294) contains the catalytic/regulato

94 This protein (Swiss-Prot entry Q05957) is synthesized in the senescent

95 sequence identity with the OAH (An07g08390, Swiss-Prot entry Q2L887, 57% identity), we produced the

96 -fold thioesterase THEM2 from human (hTHEM2; Swiss-Prot entry Q9NPJ3 ).

97 The PDB, SWISS-PROT, ENZYME, and CATH databases have been importe

98 ng proteins (AfCS), eukaryotic proteins from SWISS-PROT (EU_SW) and non-homologous protein segments w

99 apped-BLAST analysis of all sequences in the SWISS-PROT family of databases.

100 , including HGMD, OMIM, ClinVar, and UniProt/Swiss-Prot, followed by an overview of the computational

101 OSTA, and recommend changes to the UniProtKB/Swiss-Prot format, which would facilitate text-mining of

102 interface to parsing and modifying files in SWISS-PROT format.

103 antly from the background of all residues in SWISS-PROT, from the group of surface residues, and from

104 two sections, corresponding to the familiar Swiss-Prot (fully manually curated entries) and TrEMBL (

105 onstrate that the vast majority of UniProtKB/Swiss-Prot functional annotations are of high quality, a

106 The SWISS-PROT group at EBI has developed the Proteome Analy

107 The SWISS-PROT group at the EBI has developed the Proteome A

108 The CSA can be queried via Swiss-Prot identifier and EC number, as well as by PDB c

109 otein sequence with homologous proteins from SWISS-PROT; (iii) matching against human EST sequences.

110 Swiss-Prot, in turn, relies on GenBank/Embl/DDJP for pre

111 quences from web sources such as GenBank and SWISS-PROT into the database.

112 (2) SWISS-PROT is more incomplete than we expected in that v

113 inference through automatic text analysis of SWISS-PROT keywords (LOCkey) and de novo prediction thro

114 ons, stored in the database (EC identifiers, SWISS-PROT keywords and information from the Enzyme data

115 lly automated method for lexical analysis of SWISS-PROT keywords that assigns sub-cellular localizati

116 define domain folds and a thesaurus based on SWISS-PROT keywords to define functional categories.

117 alization through automatic text analysis of SWISS-PROT keywords; and (iv) LOC3Dini, ab initio predic

118 The TrEMBL database contains together with SWISS-PROT nearly all publicly available protein sequenc

119 o obtain sequence mapping between entries in Swiss-Prot, OMIM and entries in PDB.

120 o other databases are provided (e.g. Entrez, SWISS-PROT, OMIM, PubMed, PubMed Central).

121 ilable protein sequences, but in contrast to SWISS-PROT only limited functional annotation.

122 h the taxonomy tree and access corresponding SWISS-PROT protein entries.

123 One of the distinguishing criteria of the SWISS-PROT protein sequence data bank is minimal redunda

124 nces, Protein Information Resource (PIR) and SWISS-PROT protein sequence database feature table annot

125 The EBI also maintains and distributes the SWISS-PROT Protein Sequence database, in collaboration w

126 NEWT is a new taxonomy portal to the SWISS-PROT protein sequence knowledgebase.

127 The annotations of GenBank and SWISS-PROT proteins are available to the public at the G

128 s of more than 200,000 non-redundant PIR and SWISS-PROT proteins organized with more than 28,000 supe

129 For 546,000 Swiss-Prot proteins, we found that 44-54% of the proteom

130 other data providers such as NCBI, RIKEN and SWISS-PROT provides standardization of gene:sequence ass

131 s found to be related based on LocusLink and SWISS-PROT references and sequence and taxonomy data.

132 Functional information in SWISS-PROT results, primarily, from assessment of articl

133 A search for CAAX box proteins from Swiss-Prot revealed more than 300 peptides.

134 comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniPr

135 The SWISS-PROT sequence database contains keywords of functi

136 genes do not exactly match the corresponding SWISS-PROT sequences, for reasons that include missing o

137 lL and R272P) was performed using the online Swiss-Prot server for automated modeling and analyzed an

138 As a cross-validation to Swiss-Prot shows, errors in protein descriptions, commen

139 rature and curated in collaboration with the Swiss-Prot team, making intensive use of controlled voca

140 roposed method on all SAPs obtained from the Swiss-Prot, the method achieves 0.42 MCC with 73.2% over

141 tomated analysis of annotations in UniProtKB/Swiss-Prot to enable groups of proteins already annotate

142 other databases (NCBI, Sanger Institute and SWISS-PROT) to provide standardization and interconnecti

143 er EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and

144 information in EpoDB obtained from GenBank, SWISS-PROT, Transfac, TRRD and GERD is curated to provid

145 tabase offers an automatic classification of SWISS-PROT+TrEMBL proteins into groups of related protei

146 available for organisms were aligned against SWISS-PROT, TrEMBL and PDB.

147 in sequences and functional information, the Swiss-Prot, TrEMBL and PIR protein database activities h

148 al annotations to the UniProt Knowledgebase (Swiss-Prot, TrEMBL and PIR-PSD) using the standardized v

149 We have studied the relationships among SWISS-PROT, TrEMBL, and GenBank with two goals.

150 tated using BLAST search against the Aracyc, Swiss-Prot, TrEMBL, gene ontology and clusters of orthol

151 Searches of all SWISS-PROT, TrEMBL, Genpept and Ensembl protein database

152 out 800 000 proteins collected from PIR-PSD, SWISS-PROT, TrEMBL, GenPept, RefSeq and PDB, with compos

153 ies from the following annotation databases: Swiss-Prot, TrEMBL, NREF, PIR, Gene Ontology, KEGG, Entr

154 of more than 1 000 000 entries from PIR-PSD, SWISS-PROT, TrEMBL, RefSeq, GenPept, and PDB.

155 utomated process, based on protein data from Swiss-Prot/TrEMBL (UniProt) and the associated mRNA data

156 through four distinct options: (i) entering Swiss-Prot/TrEMBL accession numbers; (ii) uploading a lo

157 126 unique protein sequences in the complete Swiss-Prot/TrEMBL database (August 25, 2003); only model

158 and their targeting signals from the PDB and SWISS-PROT/TrEMBL databases.

159 genome have identical sequence matches with SWISS-PROT/TrEMBL sequences, 13.4% have exact substring

160 es and easy links to the major protein (PDB, SWISS-PROT/TrEMBL, PIR-ALN, NCBI Taxonomy Browser) and l

161 of which are ORFs) have no clear matches to SWISS-PROT/TrEMBL.

162 ta relevant to red blood cells from GenBank, SWISS-PROT, TRRD (transcriptional regulation data) and G

163 he result of an iterative database search in SWISS-PROT using a position-weighted dynamic programming

164 s, the curated tissue specificity offered in SWISS-PROT was accurate in 78% of cases.

165 ted as having the same function in UniProtKB/Swiss-Prot which can be used for large-scale analysis.

166 sers can reliably identify those proteins in SWISS-PROT whose functions were determined experimentall

167 NPs in dbSNP and amino acid substitutions in Swiss-Prot with protein structural information, if avail

168 NPs in dbSNP and amino acid substitutions in Swiss-Prot with protein structural information, links to