EMGLib: the Enhanced Microbial Genomes Library (update 2000)

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1999 Dec 11

PMID 10592183

Citations 7

Authors

G Perriere

P Bessieres

B Labedan

Affiliations

Soon will be listed here.

Abstract

As the number of complete microbial genomes publicly available is still growing, the problem of annotation quality in these very large sequences remains unsolved. Indeed, the number of annotations associated with complete genomes is usually lower than those of the shorter entries encountered in the repository collections. Moreover, classical sequence database management systems have difficulties in handling entries of such size. In this context, the Enhanced Microbial Genomes Library (EMGLib) was developed to try to alleviate these problems. This library contains all the complete genomes from prokaryotes (bacteria and archaea) already sequenced and the yeast genome in GenBank format. The annotations are improved by the introduction of data on codon usage, gene orientation on the chromosome and gene families. It is possible to access EMGLib through two database systems set up on WWW servers: the PBIL server at http://pbil.univ-lyon1.fr/emglib.html and the MICADO server at http://locus.jouy.inra.fr/micado

Citing Articles

Codon usage domains over bacterial chromosomes.

Bailly-Bechet M, Danchin A, Iqbal M, Marsili M, Vergassola M PLoS Comput Biol. 2006; 2(4):e37.

PMID: 16683018 PMC: 1447655. DOI: 10.1371/journal.pcbi.0020037.

Evolutionary origins of genomic repertoires in bacteria.

Lerat E, Daubin V, Ochman H, Moran N PLoS Biol. 2005; 3(5):e130.

PMID: 15799709 PMC: 1073693. DOI: 10.1371/journal.pbio.0030130.

Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli.

Daubin V, Ochman H Genome Res. 2004; 14(6):1036-42.

PMID: 15173110 PMC: 419781. DOI: 10.1101/gr.2231904.

The source of laterally transferred genes in bacterial genomes.

Daubin V, Lerat E, Perriere G Genome Biol. 2003; 4(9):R57.

PMID: 12952536 PMC: 193657. DOI: 10.1186/gb-2003-4-9-r57.

Integrated databanks access and sequence/structure analysis services at the PBIL.

Perriere G, Combet C, Penel S, Blanchet C, Thioulouse J, Geourjon C Nucleic Acids Res. 2003; 31(13):3393-9.

PMID: 12824334 PMC: 168937. DOI: 10.1093/nar/gkg530.

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