Abstract
The taxonomically broad organelle genome database (GOBASE) organizes and integrates diverse data related to organelles (mitochondria and chloroplasts). The current version of GOBASE focuses on the mitochondrial subset of data and contains molecular sequences, RNA secondary structures and genetic maps, as well as taxonomic information for all eukaryotic species represented. The database has been designed so that complex biological queries, especially ones posed in a comparative genomics context, are supported. GOBASE has been implemented as a relational database with a web-based user interface (http://megasun.bch.umontreal.ca/gobase/gobas e.html ). Custom software tools have been written in house to assist in the population of the database, data validation, nomenclature standardization and front-end design. The database is fully operational and publicly accessible via the World Wide Web, allowing interactive browsing, sophisticated searching and easy downloading of data.
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Selected References
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- Bairoch A., Apweiler R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res. 1998 Jan 1;26(1):38–42. doi: 10.1093/nar/26.1.38. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Calò D., De Pascali A., Sasanelli D., Tanzariello F., Tommaseo Ponzetta M., Saccone C., Attimonelli M. MmtDB: a Metazoa mitochondrial DNA variants database. Nucleic Acids Res. 1997 Jan 1;25(1):200–205. doi: 10.1093/nar/25.1.200. [DOI] [PMC free article] [PubMed] [Google Scholar]
- George D. G., Dodson R. J., Garavelli J. S., Haft D. H., Hunt L. T., Marzec C. R., Orcutt B. C., Sidman K. E., Srinivasarao G. Y., Yeh L. S. The Protein Information Resource (PIR) and the PIR-International Protein Sequence Database. Nucleic Acids Res. 1997 Jan 1;25(1):24–28. doi: 10.1093/nar/25.1.24. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gutell R. R. Collection of small subunit (16S- and 16S-like) ribosomal RNA structures: 1994. Nucleic Acids Res. 1994 Sep;22(17):3502–3507. doi: 10.1093/nar/22.17.3502. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gutell R. R., Gray M. W., Schnare M. N. A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993. Nucleic Acids Res. 1993 Jul 1;21(13):3055–3074. doi: 10.1093/nar/21.13.3055. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Harger C., Skupski M., Allen E., Clark C., Crowley D., Dickinson E., Easley D., Espinosa-Lujan A., Farmer A., Fields C. The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes. Nucleic Acids Res. 1997 Jan 1;25(1):18–23. doi: 10.1093/nar/25.1.18. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Karp P. D., Riley M., Paley S. M., Pellegrini-Toole A., Krummenacker M. EcoCyc: Encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res. 1998 Jan 1;26(1):50–53. doi: 10.1093/nar/26.1.50. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kogelnik A. M., Lott M. T., Brown M. D., Navathe S. B., Wallace D. C. MITOMAP: an update on the status of the human mitochondrial genome database. Nucleic Acids Res. 1997 Jan 1;25(1):196–199. doi: 10.1093/nar/25.1.196. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rioux P. A., Gilbert W. A., Littlejohn T. G. A portable search engine and browser for the Entrez database. J Comput Biol. 1994 Winter;1(4):293–295. doi: 10.1089/cmb.1994.1.293. [DOI] [PubMed] [Google Scholar]