iMap: a database-driven utility to integrate and access the genetic and physical maps of maize
| Autor: | Edward H. Coe, Michael D. McMullen, Steve G. Schroeder, Zhiwei Fang, Hector Sanchez-Villeda, Georgia L. Davis, Seth A. Havermann, Karen C. Cone, I. Vroh Bi, Young-Sun Yim, Jack M. Gardiner, Mary L. Polacco |
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| Rok vydání: | 2003 |
| Předmět: |
Statistics and Probability
Relational database Computer science Information Storage and Retrieval Locus (genetics) Documentation computer.software_genre Biochemistry Polymorphism Single Nucleotide Zea mays Set (abstract data type) User-Computer Interface Databases Genetic Graphics Molecular Biology Bacterial artificial chromosome Internet Contig Database Accession number (library science) Information Dissemination Gene Expression Profiling food and beverages Chromosome Chromosome Mapping Sequence Analysis DNA Accession number (bioinformatics) Computer Science Applications Systems Integration Computational Mathematics Computational Theory and Mathematics Feature (computer vision) Database Management Systems User interface computer Genome Plant |
| Zdroj: | Bioinformatics (Oxford, England). 19(16) |
| ISSN: | 1367-4803 |
| Popis: | Motivation: Because of the unique biological features, a bioinformatic platform for the integrated genetic and physical map of maize is required for storing, integrating, accessing and visualizing the underlying data. Results: The goal of the Maize Mapping Project is to develop a fully integrated genetic and physical map for maize. To display this integrated map, we have developed iMap. iMap has three main components: a relational database (iMapDB), a map graphic browser (iMap Viewer) and a search utility (iMap Search). iMapDB is populated with current genetic and physical map data, describing relationships among genetic loci, molecular markers and bacterial artificial chromosome (BAC) contigs. The database also contains integrated information produced by applying a set of anchoring rules to assign BAC contigs to specific locations on the genetic map. The iMap Viewer and iMap Search functions are combined in the user interface to allow viewing and retrieving many types of genetic and physical map data. The iMap Viewer features side-by-side chromosome-based displays of the genetic map and associated BAC contigs. For each genetic locus, information about marker type or contig can be viewed via pop-up windows that feature links to external data resources. Searches can be conducted for genetic locus, probe or sequence accession number; search results include relevant map positions, anchored BAC contigs and links to the graphical display of relevant chromosomes. iMap can be accessed at http://www.maizemap.org Availability: The iMap utility package is available for non-commercial use upon request from the authors. |
| Databáze: | OpenAIRE |
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