ARS | Publication request: Imap: a Tool for the Integration of Genetic and Physical Maps

Submitted to: Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 8, 2003
Publication Date: July 1, 2003
Citation: Fang, Z., Cone, K., Sanchez, H., Polacco, M.L., Mcmullen, M.D., Schroeder, S., Gardiner, J., Davis, G., Seth, A., Yim, Y. 2003. Imap: a tool for the integration of genetic and physical maps. Bioinformatics. 19(16):2105-2111.

Interpretive Summary: Efficient and effective access to data about the maize genome is provided by a cross-connecting integrated map tool, iMap. The genome can be represented by two kinds of maps, genetic reflecting the order of genes on the chromosomes and physical reflecting the order of DNA. The importance of tying the two kinds of map together lies in the cross-referencing synergism of order in one combined with order of the other. The iMap tool presents data that are being actively produced in genetic and genomic projects for this purpose. Breeders and biotechnologists are rapidly taking advantage of the knowledge and tools of this project to access information and diversity for the advancement of maize productivity and efficiency. The present work greatly enhances and facilitates the ability of plant scientists seeking to make crop improvements as well as to understand basic biological systems, to extract current and retrospective data together, and to use them effectively.

Technical Abstract: To integrate genetic and physical maps in the Maize Mapping Project, we have developed a tool, iMap, the Integrated Genetic and Physical Map viewer (www.maizemap.org). iMap presents the genetic map, associated BAC contigs of the physical map, and access to dynamic links for information about the contigs and the markers. It operates in a database environment and contains two main components: a relational database, iMapDB, and a user interface. iMapDB is implemented in a Sybase database management system and is populated with the genetic map data from MaizeDB (www.agron.missouri.edu) and BAC contig data generated by FPC (Fingerprint Contig) fingerprint technology from the Clemson University Genomics Institute (www.genome.clemson.edu/projects/maize/fpc). The iMap user interface has been developed based on GIOT (Genome Information displayed Orderly Tool) software that was kindly provided by the Rice Genome Research Program, Tsukuba, Japan (http://rgp.dna.affrc.go.jp). In addition, the java servlet is used for communication between client and server - responding for data requests and transfers.