Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1997 Jan 1;25(1):53–56. doi: 10.1093/nar/25.1.53

The NRSub database: update 1997.

G Perrière 1, I Moszer 1, T Gojobori 1
PMCID: PMC146364  PMID: 9016504

Abstract

In the context of the international project aiming at sequencing the whole genome of Bacillus subtilis we have developed NRSub, a non-redundant database of sequences from this organism. Starting from the B.subtilis sequences available in the repository collections we have removed all encountered duplications, then we have added extra annotations to the sequences (e.g. accession numbers for the genes, locations on the genetic map, codon usage index). We have also added cross-references with EMBL/GenBank/DDBJ, MEDLINE, SWISS-PROT and ENZYME databases. NRSub is distributed through anonymous FTP as a text file in EMBL format and as an ACNUC database. It is also possible to access the database through two dedicated World Wide Web servers located in France (http://acnuc.univ-lyon1.fr/nrsub/nrsub.++ +html ) and in Japan (http://ddbjs4h.genes.nig.ac.jp/ ).

Full Text

The Full Text of this article is available as a PDF (81.2 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bairoch A., Apweiler R. The SWISS-PROT protein sequence data bank and its new supplement TREMBL. Nucleic Acids Res. 1996 Jan 1;24(1):21–25. doi: 10.1093/nar/24.1.21. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bairoch A. The ENZYME data bank in 1995. Nucleic Acids Res. 1996 Jan 1;24(1):221–222. doi: 10.1093/nar/24.1.221. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Benson D. A., Boguski M., Lipman D. J., Ostell J. GenBank. Nucleic Acids Res. 1996 Jan 1;24(1):1–5. doi: 10.1093/nar/24.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Demerec M., Adelberg E. A., Clark A. J., Hartman P. E. A proposal for a uniform nomenclature in bacterial genetics. Genetics. 1966 Jul;54(1):61–76. doi: 10.1093/genetics/54.1.61. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Devine K. M. The Bacillus subtilis genome project: aims and progress. Trends Biotechnol. 1995 Jun;13(6):210–216. doi: 10.1016/S0167-7799(00)88948-9. [DOI] [PubMed] [Google Scholar]
  6. Etzold T., Argos P. SRS--an indexing and retrieval tool for flat file data libraries. Comput Appl Biosci. 1993 Feb;9(1):49–57. doi: 10.1093/bioinformatics/9.1.49. [DOI] [PubMed] [Google Scholar]
  7. Etzold T., Argos P. Transforming a set of biological flat file libraries to a fast access network. Comput Appl Biosci. 1993 Feb;9(1):59–64. doi: 10.1093/bioinformatics/9.1.59. [DOI] [PubMed] [Google Scholar]
  8. George D. G., Barker W. C., Mewes H. W., Pfeiffer F., Tsugita A. The PIR-International Protein Sequence Database. Nucleic Acids Res. 1996 Jan 1;24(1):17–20. doi: 10.1093/nar/24.1.17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Gouy M., Gautier C., Attimonelli M., Lanave C., di Paola G. ACNUC--a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage. Comput Appl Biosci. 1985 Sep;1(3):167–172. doi: 10.1093/bioinformatics/1.3.167. [DOI] [PubMed] [Google Scholar]
  10. Harwood C. R., Wipat A. Sequencing and functional analysis of the genome of Bacillus subtilis strain 168. FEBS Lett. 1996 Jun 24;389(1):84–87. doi: 10.1016/0014-5793(96)00524-8. [DOI] [PubMed] [Google Scholar]
  11. Itaya M., Tanaka T. Complete physical map of the Bacillus subtilis 168 chromosome constructed by a gene-directed mutagenesis method. J Mol Biol. 1991 Aug 5;220(3):631–648. doi: 10.1016/0022-2836(91)90106-g. [DOI] [PubMed] [Google Scholar]
  12. Lobry J. R. Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol. 1996 May;13(5):660–665. doi: 10.1093/oxfordjournals.molbev.a025626. [DOI] [PubMed] [Google Scholar]
  13. Moszer I., Glaser P., Danchin A. SubtiList: a relational database for the Bacillus subtilis genome. Microbiology. 1995 Feb;141(Pt 2):261–268. doi: 10.1099/13500872-141-2-261. [DOI] [PubMed] [Google Scholar]
  14. Perrière G., Gouy M., Gojobori T. NRSub: a non-redundant data base for the Bacillus subtilis genome. Nucleic Acids Res. 1994 Dec 25;22(25):5525–5529. doi: 10.1093/nar/22.25.5525. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Perrière G., Thioulouse J. On-line tools for sequence retrieval and multivariate statistics in molecular biology. Comput Appl Biosci. 1996 Feb;12(1):63–69. doi: 10.1093/bioinformatics/12.1.63. [DOI] [PubMed] [Google Scholar]
  16. Rodriguez-Tomé P., Stoehr P. J., Cameron G. N., Flores T. P. The European Bioinformatics Institute (EBI) databases. Nucleic Acids Res. 1996 Jan 1;24(1):6–12. doi: 10.1093/nar/24.1.6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Sharp P. M., Li W. H. The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987 Feb 11;15(3):1281–1295. doi: 10.1093/nar/15.3.1281. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES