The Proteome Analysis database:: a tool for the in silico analysis of whole proteomes

被引：59

作者：

Pruess, M

Fleischmann, W

Kanapin, A

Karavidopoulou, Y

Kersey, P

Kriventseva, E

Mittard, V

Mulder, N

Phan, I

Servant, F

Apweiler, R

机构：

[1] European Bioinformat Inst, EMBL Outstn, Cambridge CB10 1SD, England

[2] CMU, Swiss Inst Bioinformat, CH-1211 Geneva 4, Switzerland

来源：

NUCLEIC ACIDS RESEARCH | 2003年 / 31卷 / 01期

关键词：

D O I：

10.1093/nar/gkg105

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The Proteome Analysis database (http://www.ebi.ac. uk/ proteome/) has been developed by the Sequence Database Group at EBI utilizing existing resources and providing comparative analysis of the predicted protein coding sequences of the complete genomes of bacteria, archeae and eukaryotes. Three main projects are used, InterPro, CluSTr and GO Slim, to give an overview on families, domains, sites, and functions of the proteins from each of the complete genomes. Complete proteome analysis is available for a total of 89 proteome sets. A specifically designed application enables InterPro proteome comparisons for any one proteome against any other one or more of the proteomes in the database.

引用

页码：414 / 417

页数：4

共 11 条

[1] The InterPro database, an integrated documentation resource for protein families, domains and functional sites [J].

Apweiler, R ;

Attwood, TK ;

Bairoch, A ;

Bateman, A ;

Birney, E ;

Biswas, M ;

Bucher, P ;

Cerutti, T ;

Corpet, F ;

Croning, MDR ;

Durbin, R ;

Falquet, L ;

Fleischmann, W ;

Gouzy, J ;

Hermjakob, H ;

Hulo, N ;

Jonassen, I ;

Kahn, D ;

Kanapin, A ;

Karavidopoulou, Y ;

Lopez, R ;

Marx, B ;

Mulder, NJ ;

Oinn, TM ;

Pagni, M ;

Servant, F ;

Sigrist, CJA ;

Zdobnov, EM .

NUCLEIC ACIDS RESEARCH, 2001, 29 (01) :37-40

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

Apweiler, R ;

Biswas, W ;

Fleischmann, W ;

Kanapin, A ;

Karavidopoulou, Y ;

Kersey, P ;

Kriventseva, EV ;

Mittard, V ;

Mulder, N ;

Phan, I ;

Zdobnov, E .

NUCLEIC ACIDS RESEARCH, 2001, 29 (01) :44-48

[3] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[4] The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 [J].

Bairoch, A ;

Apweiler, R .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :45-48

[5] The Protein Data Bank [J].

Berman, HM ;

Westbrook, J ;

Feng, Z ;

Gilliland, G ;

Bhat, TN ;

Weissig, H ;

Shindyalov, IN ;

Bourne, PE .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242

[6] Protein folds and families: sequence and structure alignments [J].

Holm, L ;

Sander, C .

NUCLEIC ACIDS RESEARCH, 1999, 27 (01) :244-247

[7] The Ensembl genome database project [J].

Hubbard, T ;

Barker, D ;

Birney, E ;

Cameron, G ;

Chen, Y ;

Clark, L ;

Cox, T ;

Cuff, J ;

Curwen, V ;

Down, T ;

Durbin, R ;

Eyras, E ;

Gilbert, J ;

Hammond, M ;

Huminiecki, L ;

Kasprzyk, A ;

Lehvaslaiho, H ;

Lijnzaad, P ;

Melsopp, C ;

Mongin, E ;

Pettett, R ;

Pocock, M ;

Potter, S ;

Rust, A ;

Schmidt, E ;

Searle, S ;

Slater, G ;

Smith, J ;

Spooner, W ;

Stabenau, A ;

Stalker, J ;

Stupka, E ;

Ureta-Vidal, A ;

Vastrik, I ;

Clamp, M .

NUCLEIC ACIDS RESEARCH, 2002, 30 (01) :38-41

[8] Interactive InterPro-based comparisons of proteins in whole genomes [J].

Kanapin, A ;

Apweiler, R ;

Biswas, M ;

Fleischmann, W ;

Karavidopoulou, Y ;

Kersey, P ;

Kriventseva, EV ;

Mittard, V ;

Mulder, N ;

Oinn, T ;

Phan, I ;

Servant, F ;

Zdobnov, E .

BIOINFORMATICS, 2002, 18 (02) :374-+

[9] CluSTr: a database of clusters of SWISS-PROT plus TrEMBL proteins [J].

Kriventseva, EV ;

Fleischmann, W ;

Zdobnov, EM ;

Apweiler, R .

NUCLEIC ACIDS RESEARCH, 2001, 29 (01) :33-36

[10]

Lo Conte L, 2002, NUCLEIC ACIDS RES, V30, P264

← 1 2 →