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Literature DB >> 11125045

Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes.

R Apweiler¹, M Biswas, W Fleischmann, A Kanapin, Y Karavidopoulou, P Kersey, E V Kriventseva, V Mittard, N Mulder, I Phan, E Zdobnov.

Abstract

The SWISS-PROT group at EBI has developed the Proteome Analysis Database utilising existing resources and providing comparative analysis of the predicted protein coding sequences of the complete genomes of bacteria, archaea and eukaryotes (http://www.ebi.ac. uk/proteome/). The two main projects used, InterPro and CluSTr, give a new perspective on families, domains and sites and cover 31-67% (InterPro statistics) of the proteins from each of the complete genomes. CluSTr covers the three complete eukaryotic genomes and the incomplete human genome data. The Proteome Analysis Database is accompanied by a program that has been designed to carry out InterPro proteome comparisons for any one proteome against any other one or more of the proteomes in the database.

Entities: Species

Mesh：

Substances：
Proteins
Proteome

Year: 2001 PMID： 11125045 PMCID： PMC29822 DOI： 10.1093/nar/29.1.44

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

16 in total

1. KEGG: kyoto encyclopedia of genes and genomes.

Authors: M Kanehisa; S Goto
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

2. ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons.

Authors: F Corpet; F Servant; J Gouzy; D Kahn
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

3. WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction.

Authors: R Overbeek; N Larsen; G D Pusch; M D'Souza; E Selkov; N Kyrpides; M Fonstein; N Maltsev; E Selkov
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

4. PRINTS-S: the database formerly known as PRINTS.

Authors: T K Attwood; M D Croning; D R Flower; A P Lewis; J E Mabey; P Scordis; J N Selley; W Wright
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

5. The Pfam protein families database.

Authors: A Bateman; E Birney; R Durbin; S R Eddy; K L Howe; E L Sonnhammer
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

6. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors: M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal: Nat Genet Date: 2000-05 Impact factor: 38.330

7. Significance of Z-value statistics of Smith-Waterman scores for protein alignments.

Authors: J P Comet; J C Aude; E Glémet; J L Risler; A Hénaut; P P Slonimski; J J Codani
Journal: Comput Chem Date: 1999-06-15

8. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

Authors: A Bairoch; R Apweiler
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

9. Protein folds and families: sequence and structure alignments.

Authors: L Holm; C Sander
Journal: Nucleic Acids Res Date: 1999-01-01 Impact factor: 16.971

10. Comparative genomics of the eukaryotes.

Authors: G M Rubin; M D Yandell; J R Wortman; G L Gabor Miklos; C R Nelson; I K Hariharan; M E Fortini; P W Li; R Apweiler; W Fleischmann; J M Cherry; S Henikoff; M P Skupski; S Misra; M Ashburner; E Birney; M S Boguski; T Brody; P Brokstein; S E Celniker; S A Chervitz; D Coates; A Cravchik; A Gabrielian; R F Galle; W M Gelbart; R A George; L S Goldstein; F Gong; P Guan; N L Harris; B A Hay; R A Hoskins; J Li; Z Li; R O Hynes; S J Jones; P M Kuehl; B Lemaitre; J T Littleton; D K Morrison; C Mungall; P H O'Farrell; O K Pickeral; C Shue; L B Vosshall; J Zhang; Q Zhao; X H Zheng; S Lewis
Journal: Science Date: 2000-03-24 Impact factor: 47.728

26 in total

1. CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins.

Authors: E V Kriventseva; W Fleischmann; E M Zdobnov; R Apweiler
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

Review 2. EBI databases and services.

Authors: P Rodriguez-Tomé
Journal: Mol Biotechnol Date: 2001-07 Impact factor: 2.695

Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes.

1. KEGG: kyoto encyclopedia of genes and genomes.

2. ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons.

3. WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction.

4. PRINTS-S: the database formerly known as PRINTS.

5. The Pfam protein families database.

6. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

7. Significance of Z-value statistics of Smith-Waterman scores for protein alignments.

8. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

9. Protein folds and families: sequence and structure alignments.

10. Comparative genomics of the eukaryotes.

1. CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins.

Review 2. EBI databases and services.

3. The identification of functional modules from the genomic association of genes.

4. Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database.

5. The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.

6. Gene3D: structural assignments for the biologist and bioinformaticist alike.

7. Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters.

8. NEWT, a new taxonomy portal.

9. The comparative proteomics of ubiquitination in mouse.

10. The mouse secretome: functional classification of the proteins secreted into the extracellular environment.