MagnaportheDB: A federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea

Stanton L. Martin, Barbara P. Blackmon, Ravi Rajagopalan, Thomas D. Houfek, Robert G. Sceeles, Sheila O. Denn, Thomas K. Mitchell, Douglas E. Brown, Rod A. Wing, Ralph A. Dean

Research output: Contribution to journalArticle

29 Scopus citations

Abstract

We have created a federated database for genome studies of Magnaporthe grisea, the causal agent of rice blast disease, by integrating end sequence data from BAC clones, genetic marker data and BAC contig assembly data. A library of 9216 BAC clones providing >25-fold coverage of the entire genome was end sequenced and fingerprinted by HindIII digestion. The Image/FPC software package was then used to generate an assembly of 188 contigs covering >95% of the genome. The database contains the results of this assembly integrated with hybridization data of genetic markers to the BAC library. AceDB was used for the core database engine and a MySQL relational database, populated with numerical representations of BAC clones within FPC contigs, was used to create appropriately scaled images. The database is being used to facilitate sequencing efforts. The database also allows researchers mapping known genes or other sequences of interest, rapid and easy access to the fundamental organization of the M.grisea genome. This database, MagnaportheDB, can be accessed on the web at http://www.cals.ncsu.edu/fungalnomics/mgdatabase/int.htm.

Original languageEnglish (US)
Pages (from-to)121-124
Number of pages4
JournalNucleic acids research
Volume30
Issue number1
DOIs
StatePublished - Jan 1 2002

ASJC Scopus subject areas

  • Genetics

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    Martin, S. L., Blackmon, B. P., Rajagopalan, R., Houfek, T. D., Sceeles, R. G., Denn, S. O., Mitchell, T. K., Brown, D. E., Wing, R. A., & Dean, R. A. (2002). MagnaportheDB: A federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea. Nucleic acids research, 30(1), 121-124. https://doi.org/10.1093/nar/30.1.121