Escherichia coli K-12:: a cooperatively developed annotation snapshot -: 2005

被引:400
作者
Riley, M [1 ]
Abe, T
Arnaud, MB
Berlyn, MKB
Blattner, FR
Chaudhuri, RR
Glasner, JD
Horiuchi, T
Keseler, IM
Kosuge, T
Mori, H
Perna, NT
Plunkett, G
Rudd, KE
Serres, MH
Thomas, GH
Thomson, NR
Wishart, D
Wanner, BL
机构
[1] Josephine Bay Paul Ctr, Marine Biol Lab, Woods Hole, MA 02543 USA
[2] Res Org Informat & Syst, Ctr Informat Biol, Mishima, Shizuoka 4118540, Japan
[3] Res Org Informat & Syst, DNA Data Bank Japan, Natl Inst Genet, Mishima, Shizuoka 4118540, Japan
[4] Stanford Univ, Dept Genet, Candida Genome Database, Sch Med, Stanford, CA 94305 USA
[5] Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT 06520 USA
[6] Univ Wisconsin, Genome Ctr Wisconsin, Madison, WI 53706 USA
[7] Univ Birmingham, Div Immun & Infect, Birmingham B15 2TT, W Midlands, England
[8] Natl Inst Basic Biol, Okazaki, Aichi 4448585, Japan
[9] SRI Int, Menlo Pk, CA 94025 USA
[10] Nara Inst Sci & Technol, Grad Sch Biol Sci, Nara 6300101, Japan
[11] Keio Univ, Inst Adv Biosci, Yamagata 9970017, Japan
[12] Univ Miami, Dept Biochem & Mol Biol, Miller Sch Med, Miami Beach, FL 33140 USA
[13] Univ York, Dept Biol, York YO10 5YW, N Yorkshire, England
[14] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England
[15] Univ Alberta, Dept Comp Sci & Biol Sci, Edmonton, AB T6G 2E8, Canada
[16] Purdue Univ, Dept Biol Sci, W Lafayette, IN 47907 USA
基金
美国国家科学基金会; 英国惠康基金; 美国国家卫生研究院; 英国生物技术与生命科学研究理事会;
关键词
D O I
10.1093/nar/gkj405
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 goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. Annotation of the genome of an organism entails identification of genes, the boundaries of genes in terms of precise start and end sites, and description of the gene products. Known and predicted functions were assigned to each gene product on the basis of experimental evidence or sequence analysis. Since both kinds of evidence are constantly expanding, no annotation is complete at any moment in time. This is a snapshot analysis based on the most recent genome sequences of two E.coli K-12 bacteria. An accurate and up-to-date description of E.coli K-12 genes is of particular importance to the scientific community because experimentally determined properties of its gene products provide fundamental information for annotation of innumerable genes of other organisms. Availability of the complete genome sequence of two K-12 strains allows comparison of their genotypes and mutant status of alleles.
引用
收藏
页码:1 / 9
页数:9
相关论文
共 46 条
[1]   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
[2]  
BABA T, 2006, IN PRESS MOL SYST BI
[3]  
BACHMANN BJ, 1996, ESCHERICHIA COLI SAL, P2460
[4]  
Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkp985, 10.1093/nar/gkr1065, 10.1093/nar/gkh121]
[5]   Improved prediction of signal peptides: SignalP 3.0 [J].
Bendtsen, JD ;
Nielsen, H ;
von Heijne, G ;
Brunak, S .
JOURNAL OF MOLECULAR BIOLOGY, 2004, 340 (04) :783-795
[6]  
BERLYN MKB, 1996, ESCHERICHIA COLI SAL, P2489
[7]   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
[8]   GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses [J].
Besemer, J ;
Borodovsky, M .
NUCLEIC ACIDS RESEARCH, 2005, 33 :W451-W454
[9]   The complete genome sequence of Escherichia coli K-12 [J].
Blattner, FR ;
Plunkett, G ;
Bloch, CA ;
Perna, NT ;
Burland, V ;
Riley, M ;
ColladoVides, J ;
Glasner, JD ;
Rode, CK ;
Mayhew, GF ;
Gregor, J ;
Davis, NW ;
Kirkpatrick, HA ;
Goeden, MA ;
Rose, DJ ;
Mau, B ;
Shao, Y .
SCIENCE, 1997, 277 (5331) :1453-+
[10]   The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 [J].
Boeckmann, B ;
Bairoch, A ;
Apweiler, R ;
Blatter, MC ;
Estreicher, A ;
Gasteiger, E ;
Martin, MJ ;
Michoud, K ;
O'Donovan, C ;
Phan, I ;
Pilbout, S ;
Schneider, M .
NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :365-370